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A primer to metabarcoding surveys of Antarctic terrestrial biodiversity

  • Paul Czechowski (a1) (a2), Laurence J. Clarke (a1) (a3) (a4), Alan Cooper (a1) and Mark I. Stevens (a5) (a6)

Ice-free regions of Antarctica are concentrated along the coastal margins but are scarce throughout the continental interior. Environmental changes, including the introduction of non-indigenous species, increasingly threaten these unique habitats. At the same time, the unique biotic communities subsisting in isolation across the continent are difficult to survey due to logistical constraints, sampling challenges and problems related to the identification of small and cryptic taxa. Baseline biodiversity data from remote Antarctic habitats are still missing for many parts of the continent but are critical to the detection of community changes over time, including newly introduced species. Here we review the potential of standardized (non-specialist) sampling in the field (e.g. from soil, vegetation or water) combined with high-throughput sequencing (HTS) of bulk DNA as a possible solution to overcome some of these problems. In particular, HTS metabarcoding approaches benefit from being able to process many samples in parallel, while workflow and data structure can stay highly uniform. Such approaches have quickly gained recognition and we show that HTS metabarcoding surveys are likely to play an important role in continent-wide biomonitoring of all Antarctic terrestrial habitats.

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Ahn, J.H., Kim, B.Y., Song, J. & Weon, H.Y. 2012. Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities. Journal of Microbiology, 50, 10711074.
Altermann, S., Leavitt, S.D., Goward, T., Nelsen, M.P. & Lumbsch, H.T. 2014. How do you solve a problem like Letharia? A new look at cryptic species in lichen-forming fungi using Bayesian clustering and SNPs from multilocus sequence data. PLoS ONE, 9, 10.1371/journal.pone.0097556.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215, 403410.
Anders, S. & Huber, W. 2010. Differential expression analysis for sequence count data. Genome Biology, 11, 10.1186/gb-2010-11-10-r106.
Ascher, J., Ceccherini, M.T., Pantani, O.L., Agnelli, A., Borgogni, F., Guerri, G., Nannipieri, P. & Pietramellara, G. 2009. Sequential extraction and genetic fingerprinting of a forest soil metagenome. Applied Soil Ecology, 42, 10.1016/j.apsoil.2009.03.005.
Aylagas, E., Borja, Á. & Rodríguez-Ezpeleta, N. 2014. Environmental status assessment using DNA metabarcoding: towards a genetics based marine biotic index (gAMBI). PLoS ONE, 9, 10.1371/journal.pone.0090529.
Bellemain, E., Davey, M.L., Kauserud, H., Epp, L.S., Boessenkool, S., Coissac, E., Geml, J., Edwards, M., Willerslev, E., Gussarova, G., Taberlet, P. & Brochmann, C. 2013. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology, 15, 11761189.
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Sayers, E.W. 2011. GenBank. Nucleic Acids Research, 39, 10.1093/nar/gkq1079.
Bik, H.M., Porazinska, D.L., Creer, S., Caporaso, J.G., Knight, R. & Thomas, W.K. 2012a. Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution, 27, 233243.
Bik, H.M., Sung, W., De Ley, P., Baldwin, J.G., Sharma, J., Rocha-Olivares, A. & Thomas, W.K. 2012b. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Molecular Ecology, 21, 10481059.
Binladen, J., Gilbert, M.T.P., Bollback, J.P., Panitz, F., Bendixen, C., Nielsen, R. & Willerslev, E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE, 2, 10.1371/journal.pone.0000197.
Bintanja, R., Severijns, C., Haarsma, R. & Hazeleger, W. 2014. The future of Antarctica’s surface winds simulated by a high-resolution global climate model: 2. Drivers of 21st century changes. Journal of Geophysical Research - Atmospheres, 119, 71607178.
Blanchet, F.G., Legendre, P., Bergeron, J.A.C. & He, F.L. 2014. Consensus RDA across dissimilarity coefficients for canonical ordination of community composition data. Ecological Monographs, 84, 10.1890/13-0648.1.
Bockheim, J.G. 1997. Properties and classification of cold desert soils from Antarctica. Soil Science Society of America Journal, 61, 224231.
Bohmann, K., Evans, A., Gilbert, M.T.P., Carvalho, G.R., Creer, S., Knapp, M., Yu, D.W. & de Bruyn, M. 2014. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 29, 358367.
Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., Mills, D.A. & Caporaso, J.G. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 10, 10.1038/NMETH.2276.
Bottos, E.M., Scarrow, J.W., Archer, S.D.J., McDonald, I.R. & Cary, S.C. 2014a. Bacterial community structures of Antarctic soils. In Cowan, D.A., ed. Antarctic terrestrial microbiology. Berlin: Springer, 933.
Bottos, E.M., Woo, A.C., Zawar-Reza, P., Pointing, S.B. & Cary, S.C. 2014b. Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica. Microbial Ecology, 67, 120128.
Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P. & Coissac, E. 2016. OBITools: a UNIX-inspired software package for DNA metabarcoding. Molecular Ecology Resources, 16, 176182.
Bragg, L.M., Stone, G., Butler, M.K., Hugenholtz, P. & Tyson, G.W. 2013. Shining a light on dark sequencing: characterising errors in ion torrent PGM data. PLoS Computational Biology, 9, 10.1371/journal.pcbi.1003031.
Bybee, S.M., Bracken-Grissom, H., Haynes, B.D., Hermansen, R.A., Byers, R.L., Clement, M.J., Udall, J.A., Wilcox, E.R. & Crandall, K.A. 2011. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biology and Evolution, 3, 13121323.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335336.
Carpenter, E.J., Lin, S.J. & Capone, D.G. 2000. Bacterial activity in South Pole snow. Applied and Environmental Microbiology, 66, 10.1128/AEM.66.10.4514-4517.2000.
Caruso, T., Trokhymets, V., Bargagli, R. & Convey, P. 2013. Biotic interactions as a structuring force in soil communities: evidence from the micro-arthropods of an Antarctic moss model system. Oecologia, 172, 10.1007/s00442-012-2503-9.
CBOL Plant Working Group . 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106, 12 79412 797.
Chown, S.L., Clarke, A., Fraser, C.I., Cary, S.C., Moon, K.L. & McGeoch, M.A. 2015a. The changing form of Antarctic biodiversity. Nature, 522, 10.1038/nature14505.
Chown, S.L., Hodgins, K.A., Griffin, P.C., Oakeshott, J.G., Byrne, M. & Hoffmann, A.A. 2015b. Biological invasions, climate change and genomics. Evolutionary Applications, 8, 10.1111/eva.12234.
Chown, S., Huiskes, A.H.L., Gremmen, N.J.M., Lee, J.E., Terauds, A., Crosbie, K., Frenot, Y., Hughes, K.A., Imura, S., Kiefer, K., Lebouvier, M., Raymond, B., Tsujimoto, M., Ware, C., van de Vijver, B. & Bergstrom, D.M. 2012a. Continent-wide risk assessment for the establishment of nonindigenous species in Antarctica. Proceedings of the National Academy of Sciences of the United States of America, 109, 10.1073/pnas.1119787109.
Chown, S.L., Lee, J.E., Hughes, K.A., Barnes, J., Barrett, P.J., Bergstrom, D.M., Convey, P., Cowan, D.A., Crosbie, K., Dyer, G., Frenot, Y., Grant, S.M., Herr, D., Kennicutt, M.C., Lamers, M., Murray, A., Possingham, H.P., Reid, K., Riddle, M.J., Ryan, P.G., Sanson, L., Shaw, J.D., Sparrow, M.D., Summerhayes, C., Terauds, A. & Wall, D.H. 2012b. Challenges to the future conservation of the Antarctic. Science, 337, 158159.
Clarke, L.J., Soubrier, J., Weyrich, L.S. & Cooper, A. 2014a. Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Molecular Ecology Resources, 14, 11601170.
Clarke, L.J., Czechowski, P., Soubrier, J., Stevens, M.I. & Cooper, A. 2014b. Modular tagging of amplicons using a single PCR for high-throughput sequencing. Molecular Ecology Resources, 14, 117121.
Cline, J., Braman, J.C. & Hogrefe, H.H. 1996. PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Research, 24, 35463551.
Coissac, E., Riaz, T. & Puillandre, N. 2012. Bioinformatic challenges for DNA metabarcoding of plants and animals. Molecular Ecology, 21, 18341847.
Colesie, C., Gommeaux, M., Green, T.G.A. & Bueddel, B. 2014. Biological soil crusts in Continental Antarctica: Garwood Valley, southern Victoria Land, and Diamond Hill, Darwin Mountains region. Antarctic Science, 26, 115123.
Convey, P. 1997. How are the life history strategies of Antarctic terrestrial invertebrates influenced by extreme environmental conditions? Journal of Thermal Biology, 22, 10.1016/S0306-4565(97)00062-4.
Convey, P. 2010. Terrestrial biodiversity in Antarctica – Recent advances and future challenges. Polar Science, 4, 135147.
Convey, P. & Stevens, M.I. 2007. Antarctic biodiversity. Science, 317, 18771878.
Convey, P., Stevens, M.I., Hodgson, D.A., Smellie, J.L., Hillenbrand, C.D., Barnes, D.K.A., Clarke, A., Pugh, P.J.A., Linse, K. & Cary, S.C. 2009. Exploring biological constraints on the glacial history of Antarctica. Quaternary Science Reviews, 28, 30353048.
Convey, P., Chown, S.L., Clarke, A., Barnes, D.K.A., Bokhorst, S., Cummings, V., Ducklow, H.W., Frati, F., Green, T.G.A., Gordon, S., Griffiths, H.J., Howard-Williams, C., Huiskes, A.H.L., Laybourn-Parry, J., Lyons, W.B., McMinn, A., Morley, S.A., Peck, L.S., Quesada, A., Robinson, S.A., Schiaparelli, S. & Wall, D.H. 2014. The spatial structure of Antarctic biodiversity. Ecological Monographs, 84, 203244.
Cowan, D.A., Ramond, J.B., Makhalanyane, T. & de Maayer, P. 2015. Metagenomics of extreme environments. Current Opinion in Microbiology, 25, 10.1016/j.mib.2015.05.005.
Czechowski, P., Clarke, L.J., Breen, J., Cooper, A. & Stevens, M.I. 2016. Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing. Soil Biology & Biochemistry, 95, 10.1016/j.soilbio.2015.12.013.
Dalén, L., Götherström, A., Meijer, T. & Shapiro, B. 2007. Recovery of DNA from footprints in the snow. Canadian Field-Naturalist, 121, 321324.
De Cárcer, D.A., Denman, S.E., McSweeney, C. & Morrison, M. 2011. Strategy for modular tagged high-throughput amplicon sequencing. Applied and Environmental Microbiology, 77, 63106312.
Deagle, B.E., Jarman, S.N., Coissac, E., Pompanon, F. & Taberlet, P. 2014. DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biology Letters, 10, 10.1098/rsbl.2014.0562.
Delmont, T.O., Simonet, P. & Vogel, T.M. 2013. Mastering methodological pitfalls for surviving the metagenomic jungle. BioEssays, 35, 744754.
Delmont, T.O., Robe, P., Cecillon, S., Clark, I.M., Constancias, F., Simonet, P., Hirsch, P.R. & Vogel, T.M. 2011. Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology, 77, 10.1128/AEM.01526-10.
Denonfoux, J., Parisot, N., Dugat-Bony, E., Biderre-Petit, C., Boucher, D., Morgavi, D.P., Le Paslier, D., Peyretaillade, E. & Peyret, P. 2013. Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration. DNA Research, 20, 185196.
Dornelas, M., Gotelli, N.J., McGill, B., Shimadzu, H., Moyes, F., Sievers, C. & Magurran, A.E. 2014. Assemblage time series reveal biodiversity change but not systematic loss. Science, 344, 10.1126/science.1248484.
Dreesens, L.L., Lee, C.K. & Cary, S.C. 2014. The distribution and identity of edaphic fungi in the McMurdo Dry Valleys. Biology, 3, 10.3390/biology3030466.
Drummond, A.J., Newcomb, R.D., Buckley, T.R., Xie, D., Dopheide, A., Potter, B.C.M., Heled, J., Ross, H.A., Tooman, L., Grosser, S., Park, D., Demetras, N.J., Stevens, M.I., Russell, J.C., Anderson, S.H., Carter, A. & Nelson, N. 2015. Evaluating a multigene environmental DNA approach for biodiversity assessment. GigaScience, 4, 10.1186/s13742-015-0086-1.
Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 24602461.
Edgar, R.C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10, 996998.
Ellis, N., Smith, S.J. & Pitcher, C.R. 2012. Gradient forests: calculating importance gradients on physical predictors. Ecology, 93, 156168.
Epp, L.S., Boessenkool, S., Bellemain, E.P., Haile, J., Esposito, A., Riaz, T., Erseus, C., Gusarov, V.I., Edwards, M.E., Johnsen, A., Stenoien, H.K., Hassel, K., Kauserud, H., Yoccoz, N.G., Brathen, K., Willerslev, E., Taberlet, P., Coissac, E. & Brochmann, C. 2012. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology, 21, 18211833.
Ettema, C.H. & Wardle, D.A. 2002. Spatial soil ecology. Trends in Ecology & Evolution, 17, 177183.
Faircloth, B.C. & Glenn, T.C. 2012. Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels. PLoS ONE, 7, 10.1371/journal.pone.0042543.
Faircloth, B.C., McCormack, J.E., Crawford, N.G., Harvey, M.G., Brumfield, R.T. & Glenn, T.C. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology, 61, 10.1093/sysbio/sys004.
Fell, J.W., Scorzetti, G., Connell, L. & Craig, S. 2006. Biodiversity of micro-eukaryotes in Antarctic Dry Valley soils with <5% soil moisture. Soil Biology & Biochemistry, 38, 31073119.
Feng, Y.-J., Liu, Q.-F., Chen, M.-Y., Liang, D. & Zhang, P. 2015. Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly. Molecular Ecology Resources, 16, 10.1111/1755-0998.12429.
Fernández-Mendoza, F., Domaschke, S., García, M.A, Jordan, P., Martín, M.P. & Printzen, C. 2011. Population structure of mycobionts and photobionts of the widespread lichen Cetraria aculeata . Molecular Ecology, 20, 12081232.
Ficetola, G.F., Pansu, J., Bonin, A., Coissac, E., Giguet-Covex, C., De Barba, M., Gielly, L., Lopes, C.M., Boyer, F., Pompanon, F., Raye, G. & Taberlet, P. 2015. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular Ecology Resources, 15, 543556.
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.
Frenot, Y., Chown, S.L., Whinam, J., Selkirk, P.M., Convey, P., Skotnicki, M. & Bergstrom, D.M. 2005. Biological invasions in the Antarctic: extent, impacts and implications. Biological Reviews, 80, 4572.
Gagné, S.A. & Proulx, R. 2009. Accurate delineation of biogeographical regions depends on the use of an appropriate distance measure. Journal of Biogeography, 36, 561562.
Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J. & Nekrutenko, A. 2005. Galaxy: a platform for interactive large-scale genome analysis. Genome Research, 15, 14511455.
Gilbert, J.A, Meyer, F., Antonopoulos, D., Balaji, P., Brown, C.T., Desai, N., Eisen, J.A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, A., Shade, A. & Stevens, R. 2010. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Standards in Genomic Sciences, 3, 243248.
Glenn, T.C. 2011. Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 10.1111/j.1755-0998.2011.03024.x.
Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D.B., Lander, E.S. & Nusbaum, C. 2009. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology, 27, 182189.
Gokul, J.K., Valverde, A., Tuffin, M., Cary, S.C. & Cowan, D.A. 2013. Micro-eukaryotic diversity in hypolithons from Miers Valley, Antarctica. Biology, 2, 331340.
Goordial, J., Davila, A., Greer, C.W., Cannam, R., DiRuggiero, J., McKay, C.P. & Whyte, L.G. 2016. Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert. Environmental Microbiology, 10.1111/1462-2920.13353.
Gutt, J., Zurell, D., Bracegridle, T.J., Cheung, W., Clark, M.S., Convey, P., Danis, B., David, B., De Broyer, C., di Prisco, G., Griffiths, H., Laffont, R., Peck, L.S., Pierrat, B., Riddle, M.J., Saucede, T., Turner, J., Verde, C., Wang, Z.M. & Grimm, V. 2012. Correlative and dynamic species distribution modelling for ecological predictions in the Antarctic: a cross-disciplinary concept. Polar Research, 31, 10.3402/polar.v31i0.11091.
Hajibabaei, M., Spall, J.L., Shokralla, S. & van Konynenburg, S. 2012. Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology, 12, 10.1186/1472-6785-12-28.
Hamming, R.W. 1950. Error detecting and error correcting codes. Bell System Technical Journal, 29, 10.1002/j.1538-7305.1950.tb00463.x.
Headland, R.K. 2009. A chronology of Antarctic exploration, 2nd ed. Bernard Quaritch, 722 pp.
Hogg, I.D., Cary, S.C., Convey, P., Newsham, K.K., O’Donnell, A.G., Adams, B.J., Aislabie, J., Frati, F., Stevens, M.I. & Wall, D.H. 2006. Biotic interactions in Antarctic terrestrial ecosystems: are they a factor? Soil Biology & Biochemistry, 38, 30353040.
Howard-Williams, C., Peterson, D., Lyons, W.B., Cattaneo-Vietti, R. & Gordon, S. 2006. Measuring ecosystem response in a rapidly changing environment: the Latitudinal Gradient Project. Antarctic Science, 18, 465471.
Hughes, K.A. & Convey, P. 2010. The protection of Antarctic terrestrial ecosystems from inter- and intra-continental transfer of non-indigenous species by human activities: a review of current systems and practices. Global Environmental Change - Human and Policy Dimensions, 20, 10.1016/j.gloenvcha.2009.09.005.
Hughes, K.A. & Convey, P. 2012. Determining the native/non-native status of newly discovered terrestrial and freshwater species in Antarctica – current knowledge, methodology and management action. Journal of Environmental Management, 93, 5266.
Hughes, K.A., Convey, P., Maslen, N.R. & Smith, R.I.L. 2010. Accidental transfer of non-native soil organisms into Antarctica on construction vehicles. Biological Invasions, 12, 875891.
Hui, F.K.C., Taskinen, S., Pledger, S., Foster, S.D. & Warton, D.I. 2015. Model-based approaches to unconstrained ordination. Methods in Ecology and Evolution, 6, 10.1111/2041-210X.12236.
Huson, D.H. & Weber, N. 2013. Microbial community analysis using MEGAN. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, 531, 10.1016/B978-0-12-407863-5.00021-6.
Jarman, S.N., McInnes, J.C., Faux, C., Polanowski, A.M., Marthick, J., Deagle, B.E., Southwell, C. & Emmerson, L. 2013. Adélie penguin population diet monitoring by analysis of food DNA in scats. PLoS ONE, 8, 10.1371/journal.pone.0082227.
Jungblut, A.D., Vincent, W.F. & Lovejoy, C. 2012. Eukaryotes in Arctic and Antarctic cyanobacterial mats. FEMS Microbiology Ecology, 82, 416428.
Kanagawa, T. 2003. Bias and artifacts in multitemplate polymerase chain reactions (PCR). Journal of Bioscience and Bioengineering, 96, 317323.
Kennicutt, M.C., Chown, S.L., Cassano, J.J., Liggett, D., Massom, R., Peck, L.S., Rintoul, S.R., Storey, J.W.V., Vaughan, D.G., Wilson, T.J. & Sutherland, W.J. 2014. Polar research: six priorities for Antarctic science. Nature, 512, 10.1038/512023a.
Kennicutt, M.C., Chown, S.L., Cassano, J.J. et al. 2015. A roadmap for Antarctic and Southern Ocean science for the next two decades and beyond. Antarctic Science, 27, 10.1017/S0954102014000674.
Khan, N., Tuffin, M., Stafford, W., Cary, C., Lacap, D.C., Pointing, S.B. & Cowan, D. 2011. Hypolithic microbial communities of quartz rocks from Miers Valley, McMurdo Dry Valleys, Antarctica. Polar Biology, 34, 16571668.
Kircher, M., Sawyer, S. & Meyer, M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research, 40, 10.1093/nar/gkr771.
Kwok, S. 1990. Procedures to minimize PCR-product carry-over. In Innis, M.A., Gelfand, D.H. & Sninsky, J.J., eds. PCR protocols: a guide to methods and applications. San Diego, CA: Academic Press, 142145.
Lan, Y., Wang, Q., Cole, J.R. & Rosen, G.L. 2012. Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLoS ONE, 7, 10.1371/journal.pone.0032491.
Lawley, B., Ripley, S., Bridge, P. & Convey, P. 2004. Molecular analysis of geographic patterns of eukaryotic diversity in Antarctic soils. Applied and Environmental Microbiology, 70, 59635972.
Lee, C.K., Barbier, B.A., Bottos, E.M., McDonald, I.R. & Cary, S.C. 2012a. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities. ISME Journal, 6, 10.1038/ismej.2011.170.
Lee, C.K., Herbold, C.W., Polson, S.W., Wommack, K.E., Williamson, S.J., McDonald, I.R. & Cary, S.C. 2012b. Groundtruthing next-gen sequencing for microbial ecology – biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS ONE, 7, 10.1371/journal.pone.0044224.
Legendre, P. & Andersson, M.J. 1999. Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecological Monographs, 69, 10.1890/0012-9615(1999)069[0001:DBRATM]2.0.CO;2.
Lemmon, A.R., Emme, S.A. & Lemmon, E.M. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology, 61, 10.1093/sysbio/sys049.
Lenz, T.L. & Becker, S. 2008. Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci – implications for evolutionary analysis. Gene, 427, 117123.
Leray, M., Yang, J.Y., Meyer, C.P., Mills, S.C., Agudelo, N., Ranwez, V., Boehm, J.T. & Machida, R.J. 2013. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Frontiers in Zoology, 10, 10.1186/1742-9994-10-34.
Lindgreen, S. 2012. AdapterRemoval: easy cleaning of next generation sequencing reads. BMC Research Notes, 5, 10.1186/1756-0500-5-337.
Lindgreen, S., Adair, K.L. & Gardner, P.P. 2016. An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports, 6, 19233, 10.1038/srep19233.
Liu, S., Li, Y.Y., Lu, J.L., Su, X., Tang, M., Zhang, R., Zhou, L.L., Zhou, C.R., Yang, Q., Ji, Y.Q., Yu, D.W. & Zhou, X. 2013. SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons. Methods in Ecology and Evolution, 4, 11421150.
Lohse, M., Bolger, A.M., Nagel, A., Fernie, A.R., Lunn, J.E., Stitt, M. & Usadel, B. 2012. RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40, W622W627.
López-Bueno, A., Tamames, J., Velázquez, D., Moya, A., Quesada, A. & Alcamí, A. 2009. High diversity of the viral community from an Antarctic lake. Science, 326, 858861.
Machida, R.J. & Knowlton, N. 2012. PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences. PLoS ONE, 7, 10.1371/journal.pone.0046180.
Magalhaes, C., Stevens, M.I., Cary, S.C., Ball, B.A., Storey, B.C., Wall, D.H., Tuerk, R. & Ruprecht, U. 2012. At limits of life: multidisciplinary insights reveal environmental constraints on biotic diversity in Continental Antarctica. PLoS ONE, 7, 10.1371/journal.pone.0044578.
Makhalanyane, T.P., Valverde, A., Birkeland, N.K., Cary, S.C., Tuffin, I.M. & Cowan, D.A. 2013. Evidence for successional development in Antarctic hypolithic bacterial communities. ISME Journal, 7, 20802090.
Marchant, D.R. & Head, J.W. 2007. Antarctic dry valleys: microclimate zonation, variable geomorphic processes, and implications for assessing climate change on Mars. Icarus, 192, 187222.
McGaughran, A., Stevens, M.I., Hogg, I.D. & Carapelli, A. 2011. Extreme glacial legacies: a synthesis of the Antarctic springtail phylogeographic record. Insects, 2, 6282.
McGeoch, M.A., Shaw, J.D., Terauds, A., Lee, J.E. & Chown, S.L. 2015. Monitoring biological invasion across the broader Antarctic: a baseline and indicator framework. Global Environmental Change - Human and Policy Dimensions, 32, 108125.
McMurdie, P.J. & Holmes, S. 2013. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE, 8, 10.1371/journal.pone.0061217.
McMurdie, P.J. & Holmes, S. 2014. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Computational Biology, 10, 10.1371/journal.pcbi.1003531.
Meyer, M., Stenzel, U. & Hofreiter, M. 2008. Parallel tagged sequencing on the 454 platform. Nature Protocols, 3, 267278.
Nakai, R., Abe, T., Baba, T., Imura, S., Kagoshima, H., Kanda, H., Kohara, Y., Koi, A., Niki, H., Yanagihara, K. & Naganuma, T. 2012. Eukaryotic phylotypes in aquatic moss pillars inhabiting a freshwater lake in East Antarctica, based on 18S rRNA gene analysis. Polar Biology, 35, 14951504.
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.
Nielsen, U.N. & Wall, D.H. 2013. The future of soil invertebrate communities in polar regions: different climate change responses in the Arctic and Antarctic? Ecology Letters, 16, 409419.
O’Neill, E.M., Schwartz, R., Bullock, C.T., Williams, J.S., Shaffer, H.B., Aguilar-Miguel, X., Parra-Olea, G. & Weisrock, D.W. 2013. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Molecular Ecology, 22, 111129.
Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H. & Wagner, H. 2015. . Vegan: community ecology package. Available at:
Orgiazzi, A., Bianciotto, V., Bonfante, P., Daghino, S., Ghignone, S., Lazzari, A., Lumini, E., Mello, A., Napoli, C., Perotto, S., Vizzini, A., Bagella, A., Murat, C. & Girlanda, M. 2013. 454 pyrosequencing analysis of fungal assemblages from geographically distant, disparate soils reveals spatial patterning and a core mycobiome. Diversity, 5, 7398.
Pedersen, M.W., Overballe-Petersen, S., Ermini, L., Sarkissian, C.D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P.F., Bohmann, K., Cappellini, E., Schnell, I.B., Wales, N.A., Caroe, C., Campos, P.F., Schmidt, A.M.Z., Gilbert, M.T.P., Hansen, A.J., Orlando, L. & Willerslev, E. 2014. Ancient and modern environmental DNA. Philosophical Transactions of the Royal Society - Biological Sciences, B370, 10.1098/rstb.2013.0383.
Pointing, S.B. & Belnap, J. 2012. Microbial colonization and controls in dryland systems. Nature Reviews Microbiology, 10, 551562.
Powell, S.M., Bowman, J.P., Snape, I. & Stark, J.S. 2003. Microbial community variation in pristine and polluted nearshore Antarctic sediments. FEMS Microbiology Ecology, 45, 10.1016/S0168-6496(03)00135-1.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W.G., Peplies, J. & Gloeckner, F.O. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35, 71887196.
R Development Team . 2016. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. Available at:
Ratnasingham, S. & Hebert, P.D.N. 2007. BOLD: the barcode of life data system ( Molecular Ecology Notes, 7, 355364.
Riaz, T., Shehzad, W., Viari, A., Pompanon, F., Taberlet, P. & Coissac, E. 2011. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 39, 10.1093/nar/gkr732.
Robertson, C.E., Harris, J.K., Wagner, B.D., Granger, D., Browne, K., Tatem, B., Feazel, L.M., Park, K., Pace, N.R. & Frank, D.N. 2013. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics, 29, 31003101.
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. 2009. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139140.
Roesch, L.F.W., Fulthorpe, R.R., Pereira, A.B., Pereira, C.K., Lemos, L.N., Barbosa, A.D., Suleiman, A.K.A., Gerber, A.L., Pereira, M.G., Loss, A. & da Costa, E.M. 2012. Soil bacterial community abundance and diversity in ice-free areas of Keller Peninsula, Antarctica. Applied Soil Ecology, 61, 715.
Rogers, A.D. 2007. Evolution and biodiversity of Antarctic organisms: a molecular perspective. Philosophical transactions of the Royal Society - Biological sciences, B362, 21912214.
Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B. & Erlich, H.A. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA-polymerase. Science, 239, 487491.
Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., Turner, P., Parkhill, J., Loman, N.J. & Walker, A.W. 2014. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biology, 12, 10.1186/s12915-014-0087-z.
Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A, Oakley, B.B., Parks, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G., van Horn, D.J. & Weber, C.F. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 75377541.
Shaw, J.D., Terauds, A., Riddle, M.J., Possingham, H.P. & Chown, S.L. 2014. Antarctica’s protected areas are inadequate, unrepresentative, and at risk. PLoS Biology, 12, 10.1371/journal.pbio.1001888.
Shokralla, S., Singer, G.A.C. & Hajibabaei, M. 2010. Direct PCR amplification and sequencing of specimens’ DNA from preservative ethanol. BioTechniques, 48, 10.2144/000113362.
Sipos, R., Székely, A.J., Palatinszky, M., Révész, S., Márialigeti, K. & Nikolausz, M. 2007. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targeting bacterial community analysis. FEMS Microbiology Ecology, 60, 10.1111/j.1574-6941.2007.00283.x.
Smith, D.P. & Peay, K.G. 2014. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE, 9, 10.1371/journal.pone.0090234.
Stiller, M., Knapp, M., Stenzel, U., Hofreiter, M. & Meyer, M. 2009. Direct multiplex sequencing (DMPS) – a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Research, 19, 18431848.
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. 2012a. Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21, 20452050.
Taberlet, P., Prud’Homme, S.M., Campione, E., Roy, J., Miquel, C., Shehzad, W., Gielly, L., Rioux, D., Choler, P., Clement, J.C., Melodelima, C., Pompanon, F. & Coissac, E. 2012b. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology, 21, 18161820.
Tang, C.Q., Leasi, F., Obertegger, U., Kieneke, A., Barraclough, T.G. & Fontaneto, D. 2012. The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proceedings of the National Academy of Sciences of the United States of America, 109, 16 20816 212.
Terauds, A., Chown, S.L., Morgan, F., Peat, H.J., Watts, D.J., Keys, H., Convey, P. & Bergstrom, D.M. 2012. Conservation biogeography of the Antarctic. Diversity and Distributions, 18, 726741.
Turrill, W.B. 1938. The expansion of taxonomy with special reference to spermatophyta. Biological Reviews, 13, 10.1111/j.1469-185X.1938.tb00522.x.
Van Dijk, E.L., Auger, H., Jaszczyszyn, Y. & Thermes, C. 2014. Ten years of next-generation sequencing technology. Trends in Genetics, 30, 10.1016/j.tig.2014.07.001.
Van Rossum, G. & Drake, F.L. 1995. Python tutorial. Amsterdam: Centrum voor Wiskunde en Informatica.
Velasco-Castrillón, A. & Stevens, M.I. 2014. Morphological and molecular diversity at a regional scale: a step closer to understanding Antarctic nematode biogeography. Soil Biology & Biochemistry, 70, 272284.
Velasco-Castrillón, A., Gibson, J.A.E. & Stevens, M.I. 2014a. A review of current Antarctic limno-terrestrial microfauna. Polar Biology, 37, 15171531.
Velasco-Castrillón, A., Page, T.J., Gibson, J.A.E. & Stevens, M.I. 2014b. Surprisingly high levels of biodiversity and endemism amongst Antarctic rotifers uncovered with mitochondrial DNA. Biodiversity, 15, 130142.
Velasco-Castrillón, A., Schultz, M.B., Colombo, F., Gibson, J.A.E., Davies, K.A, Austin, A.D. & Stevens, M.I. 2014c. Distribution and diversity of soil microfauna from East Antarctica: assessing the link between biotic and abiotic factors. PLoS ONE, 9, 10.1371/journal.pone.0087529.
Wang, Y., Naumann, U., Wright, S.T. & Warton, D.I. 2012. mvabund – an R package for model-based analysis of multivariate abundance data. Methods in Ecology and Evolution, 3, 10.1111/j.2041-210X.2012.00190.x.
Whittaker, R.H. 1960. Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 10.2307/1943563.
Wilke, A., Bischof, J., Gerlach, W., Glass, E., Harrison, T., Keegan, K.P., Paczian, T., Trimble, W.L., Bagchi, S., Gram, A., Chaterji, S. & Meyer, F. 2016. The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Research, 44, 10.1093/nar/gkv1322.
Willerslev, E., Hansen, A.J. & Poinar, H.N. 2004. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends in Ecology & Evolution, 19, 10.1016/j.tree.2003.11.010.
Wish, M. & Carroll, J.D. 1982. Multidimensional scaling and its applications. In Krishnaiah, P.R. & Kanal, L.N., eds. Handbook of statistics 2. North-Holland: Elsevier, 317345.
Wu, T.H., Ayres, E., Bardgett, R.D., Wall, D.H. & Garey, J.R. 2011. Molecular study of worldwide distribution and diversity of soil animals. Proceedings of the National Academy of Sciences of the United States of America, 108, 17 72017 725.
Zhan, A.B., Bailey, S.A., Heath, D.D. & Macisaac, H.J. 2014. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities. Molecular Ecology Resources, 14, 10.1111/1755-0998.12254.
Zhou, X.F. & Rokas, A. 2014. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Molecular Ecology, 23, 10.1111/mec.12680.
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Antarctic Science
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