Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

Molecular Ecology - Tập 19 Số s1 - Trang 21-31 - 2010
Thorsten Stoeck1, David Bass2, Markus E. Nebel3, Richard Christen4, Meredith D. M. Jones5, Hans‐Werner Breiner1, Thomas A. Richards5
1Department of Ecology, University of Kaiserslautern, D-67653 Kaiserslautern, Germany
2Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
3Department of Computer Science, University of Kaiserslautern, D-67653 Kaiserslautern, Germany
4Université de Nice et CNRS UMR 654, Laboratoire de Biologie Virtuelle, Centre de Biochimie, Parc Valrose, Faculté des Sciences, Nice, F 06108, France
5Centre for Eukaryotic Evolutionary Microbiology, School of Biosciences, University of Exeter, Devon EX4 4QD, UK

Tóm tắt

AbstractSequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology. The results of these analyses have shown that protist groups are far more genetically heterogeneous than their morphological diversity suggests. However, the clone library approach is labour‐intensive, relatively expensive, and methodologically biased. Therefore, even the most intensive rDNA library analyses have recovered only small samples of much larger assemblages, indicating that global environments harbour a vast array of unexplored biodiversity. High‐throughput parallel tag 454 sequencing offers an unprecedented scale of sampling for molecular detection of microbial diversity. Here, we report a 454 protocol for sampling and characterizing assemblages of eukaryote microbes. We use this approach to sequence two SSU rDNA diversity markers—the variable V4 and V9 regions—from 10 L of anoxic Norwegian fjord water. We identified 38 116 V4 and 15 156 V9 unique sequences. Both markers detect a wide range of taxonomic groups but in both cases the diversity detected was dominated by dinoflagellates and close relatives. Long‐tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes. Most tags detected represent genotypes not currently in GenBank, although many are similar to database sequences. We suggest that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and we discuss the biological significance of this high amplicon diversity.

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Tài liệu tham khảo

10.1111/j.1529-8817.2005.00136.x

10.1371/journal.pone.0006372

10.1016/j.protis.2006.10.001

10.1073/pnas.77.12.7323

10.1046/j.1529-8817.2000.00010.x

10.1099/ijs.0.63229-0

10.1111/j.1744-7410.2001.tb00117.x

10.1016/j.protis.2009.01.004

10.1128/AEM.72.5.3626-3636.2006

Berney C, 2004, How many novel eukaryotic ‘kingdoms’? Pitfalls and limitations of environmental DNA surveys, BMC Evolutionary Biology, 2, 13

10.1111/j.1550-7408.2008.00381.x

10.1126/science.1164387

10.1016/j.ympev.2008.09.017

10.1093/nar/gkm233

10.1111/j.1550-7408.2005.05202006.x

10.1007/s001220100741

10.1126/science.7146895

10.1073/pnas.062186399

10.1093/oxfordjournals.molbev.a025684

10.1038/345060a0

10.1016/j.tree.2006.06.012

10.1111/j.1462-2920.2008.01731.x

10.1016/j.protis.2008.11.007

10.1111/j.1462-2920.2008.01857.x

10.1099/ijs.0.02441-0

10.1038/nrmicro1341

10.1186/gb-2007-8-7-r143

10.1086/378684

Lane DJ, 1991, Nucleic Acid Technologies in Bacterial Systematic, 115

10.1111/j.1462-2920.2006.01158.x

10.1073/pnas.0235779100

10.1038/nature03959

10.1128/AEM.68.9.4554-4558.2002

10.1128/AEM.70.6.3528-3534.2004

10.1016/0378-1119(88)90066-2

10.1038/35054541

10.1126/science.1136264

10.1126/science.276.5313.734

10.2113/0320173

10.1016/j.tim.2006.04.007

10.1128/AEM.71.3.1193-1201.2005

10.1016/j.mib.2005.04.010

10.1111/j.1462-2920.2005.00828.x

10.1073/pnas.89.8.3639

10.1016/0022-2836(74)90376-3

10.1016/j.cub.2004.08.038

10.1073/pnas.0605127103

10.3354/ame01301

10.1128/AEM.69.5.2657-2663.2003

10.1128/AEM.69.9.5656-5663.2003

10.1016/j.protis.2005.10.004

10.1371/journal.pone.0000728

10.1016/j.protis.2006.03.003

10.1093/nar/25.1.111

von Wintzingerode F, 1997, Determination of microbial diversity in environmental samples: pitfalls of PCR‐based rRNA analysis, FEMS Microbiology Ecology, 21, 213

10.1093/nar/28.23.4698

10.1016/j.femsec.2004.10.006

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Molecular Ecology

Tập 19 Số s1

21-31

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