JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Application of Amplicon Pyrosequencing in Soil Microbial Ecology
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Application of Amplicon Pyrosequencing in Soil Microbial Ecology
Ahn, Jae-Hyung; Kim, Byung-Yong; Kim, Dae-Hoon; Song, Jaekyeong; Weon, Hang-Yeon;
  PDF(new window)
 Abstract
Soil microbial communities are immensely diverse and complex with respect to species richness and community size. These communities play essential roles in agricultural soil because they are responsible for most of the nutrient cycles in the soil and influence the plant diversity and productivity. However, the majority of these microbes remain uncharacterized because of poor culturability. Next-generation sequencing techniques have revolutionized many areas of biology by providing cheaper and faster alternatives to Sanger sequencing. Among them, amplicon pyrosequencing is a powerful tool developed by 454 Life Sciences for assessing the diversity of complex microbial communities by sequencing PCR products or amplicons. This review summarizes the current opinions in amplicon sequencing of soil microbial communities, and provides practical guidance and advice on sequence quality control, aligning, clustering, OTU- and taxon-based analysis. The last section of this article includes a few representative studies conducted using amplicon pyrosequencing.
 Keywords
Next generation sequencing;Amplicon pyrosequencing;Soil microbial ecology;Microbial diversity;Community structure;
 Language
Korean
 Cited by
1.
천일염전에서 Pyrosequencing을 이용한 호염성세균의 다양성과 분리 동정에 관한 연구,박석환;이건형;

한국자연보호학회지, 2015. vol.9. 2, pp.149-156 crossref(new window)
 References
1.
Acinas, S.G., R. Sarma-Rupavtarm, V. Klepac-Ceraj, and M.F. Polz. 2005. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71:8966-8969. crossref(new window)

2.
Acosta-Martínez, V., S. Dowd, Y. Sun, and V. Allen. 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. crossref(new window)

3.
Acosta-Martínez, V., S.E. Dowd, C.W. Bell, R. Lascano, J.D. Booker, T.M. Zobeck, and D.R. Upchurch. 2010a. Microbial community composition as affected by dryland cropping systems and tillage in a semiarid sandy soil. Diversity. 2:910-931. crossref(new window)

4.
Acosta-Martínez, V., S.E. Dowd, Y. Sun, D. Wester, and V. Allen. 2010b. Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system. Appl. Soil Ecol. 45:13-25. crossref(new window)

5.
Ahn, J.H., J. Song, B.Y. Kim, M.S. Kim, J.H. Joa, and H.Y. Weon. 2012. Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices. J. Microbiol. 50:754-765. crossref(new window)

6.
Altschul, S.F., W. Gish, W. Miller, E.W. Myers, and D.J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. crossref(new window)

7.
Amann, R.I., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.

8.
Ashelford, K.E., N.A. Chuzhanova, J.C. Fry, A.J. Jones, and A.J. Weightman. 2005. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71:7724-7736. crossref(new window)

9.
Bartram, A.K., M.D.J. Lynch, J.C. Stearns, G. Moreno- Hagelsieb, and J.D. Neufeld. 2011. Generation of multimillionsequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl. Environ. Microbiol. 77:3846-3852. crossref(new window)

10.
Benson, D.A., I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, and E.W. Sayers. 2011. GenBank. Nucleic Acids Res. 39:D32-D37. crossref(new window)

11.
Caporaso, J.G., J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A.G. Pena, J.K. Goodrich, J.I. Gordon, G.A. Huttley, S.T. Kelley, D. Knights, J.E. Koenig, R.E. Ley, C.A. Lozupone, D. McDonald, B.D. Muegge, M. Pirrung, J. Reeder, J.R. Sevinsky, P.J. Tumbaugh, W.A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld, and R. Knight. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 7:335-336. crossref(new window)

12.
Caporaso, J.G., C.L. Lauber, W.A. Walters, D. Berg- Lyons, J. Huntley, N. Fierer, S.M. Owens, J. Betley, L. Fraser, M. Bauer, N. Gormley, J.A. Gilbert, G. Smith, and R. Knight. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6:1621-1624. crossref(new window)

13.
Chenna, R., H. Sugawara, T. Koike, R. Lopez, T.J. Gibson, D.G. Higgins, and J.D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500. crossref(new window)

14.
Cole, J.R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, T. Marsh, G.M. Garrity, and J.M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145. crossref(new window)

15.
Cui, J., H. Meng, M. Nie, X. Chen, Z. Li, N. Bu, B. Li, J. Chen, Z. Quan, and C. Fang. 2012. Bacterial succession during 500 years of soil development under agricultural use. Eco. Res. 27:793-807. crossref(new window)

16.
DeSantis, T.Z., P. Hugenholtz, N. Larsen, M. Rojas, E.L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G.L. Andersen. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072. crossref(new window)

17.
Dolfing, J., A. Vos, J. Bloem, P.A.I. Ehlert, N.B. Naumova, and P.J. Kuikman. 2004. Microbial diversity in archived soils. Science. 306:813-813.

18.
Edgar, R. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 5:113. crossref(new window)

19.
Edgar, R.C., B.J. Haas, J.C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 27:2194-2200. crossref(new window)

20.
Eilers, K.G., C.L. Lauber, R. Knight, and N. Fierer. 2010. Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol. Biochem. 42:896-903. crossref(new window)

21.
Garrity, G.M., T.G. Lilburn, J.R. Cole, S.H. Harrison, J. Euzeby, and B.J. Tindall. 2007. The taxonomic outline of Bacteria and Archaea. TOBA Release 7.7. 10.1601 /TOBA7.7. Michigan State University Board of Trustees, Michigan, USA.

22.
Gilles, A., E. Meglecz, N. Pech, S. Ferreira, T. Malausa, and J.F. Martin. 2011. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics. 12.

23.
Haas, B.J., D. Gevers, A.M. Earl, M. Feldgarden, D.V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S.K. Highlander, E. Sodergren, B. Methe, T.Z. DeSantis, T.H.M. Consortium, J.F. Petrosino, R. Knight, and B.W. Birren. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21:494-504. crossref(new window)

24.
Hamp, T.J., W.J. Jones, and A.A. Fodor. 2009. Effects of experimental choices and analysis noise on surveys of the "rare biosphere". Appl. Environ. Microbiol. 75:3263- 3270. crossref(new window)

25.
Hongoh, Y., H. Yuzawa, M. Ohkuma, and T. Kudo. 2003. Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiol. Lett. 221:299-304. crossref(new window)

26.
Huber, T., G. Faulkner, and P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics. 20:2317-2319. crossref(new window)

27.
Huse, S.M., J.A. Huber, H.G. Morrison, M.L. Sogin, and D.M. Welch. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8:R143. crossref(new window)

28.
Huse, S.M., L. Dethlefsen, J.A. Huber, D.M. Welch, D.A. Relman, and M.L. Sogin. 2008. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics. 4.

29.
Huse, S.M., D.M. Welch, H.G. Morrison, and M.L. Sogin. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12:1889-1898. crossref(new window)

30.
Ishii, K. and M. Fukui. 2001. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl. Environ. Microbiol. 67:3753-3755. crossref(new window)

31.
Klammer, S., C. Mondini, and H. Insam. 2005. Microbial community fingerprints of composts stored under different conditions. Annals of Microbiology. 55:299-305.

32.
Knight, R., J.G. Caporaso, C.L. Lauber, W.A. Walters, D. Berg-Lyons, C.A. Lozupone, P.J. Turnbaugh, and N. Fierer. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U.S.A. 108:4516-4522. crossref(new window)

33.
Kolton, M., Y.M. Harel, Z. Pasternak, E.R. Graber, Y. Elad, and E. Cytryn. 2011. Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl. Environ. Microbiol. 77:4924-4930. crossref(new window)

34.
Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12:118-123. crossref(new window)

35.
Lauber, C.L., M. Hamady, R. Knight, and N. Fierer. 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. crossref(new window)

36.
Lauber, C.L., N. Zhou, J.I. Gordon, R. Knight, and N. Fierer. 2010. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol. Lett. 307:80-86. crossref(new window)

37.
Li, W. and A. Godzik. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 22:1658-1659. crossref(new window)

38.
Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A.W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüßmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371. crossref(new window)

39.
Peplies, J., R. Kottmann, W. Ludwig, and F.O. Glöckner. 2008. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst. Appl. Microbiol. 31:251-257. crossref(new window)

40.
Polz, M.F. and C.M. Cavanaugh. 1998. Bias in templateto- product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.

41.
Pruesse, E., J. Peplies, and F.O. Glockner. 2012. SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics.

42.
Qiu, X., L. Wu, H. Huang, P.E. McDonel, A.V. Palumbo, J.M. Tiedje, and J. Zhou. 2001. Evaluation of PCR- generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67:880-887. crossref(new window)

43.
Quince, C., A. Lanzen, R. Davenport, and P. Turnbaugh. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 12:38. crossref(new window)

44.
Ranjard, L., D.P.H. Lejon, C. Mougel, L. Schehrer, D. Merdinoglu, and R. Chaussod. 2003. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ. Microbiol. 5:1111-1120. crossref(new window)

45.
Rochelle, P.A., B.A. Cragg, J.C. Fry, R.J. Parkes, and A.J. Weightman. 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol. Ecol. 15:215-225. crossref(new window)

46.
Rousk, J., E. Baath, P.C. Brookes, C.L. Lauber, C. Lozupone, J.G. Caporaso, R. Knight, and N. Fierer. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4:1340-1351. crossref(new window)

47.
Schloss, P.D. and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506. crossref(new window)

48.
Schloss, P.D. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE. 4:e8230. crossref(new window)

49.
Schloss, P.D., S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, E.B. Hollister, R.A. Lesniewski, B.B. Oakley, D.H. Parks, C.J. Robinson, J.W. Sahl, B. Stres, G.G. Thallinger, D.J. Van Horn, and C.F. Weber. 2009. Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537- 7541. crossref(new window)

50.
Schloss, P.D. 2010. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput. Biol. 6:e1000844. crossref(new window)

51.
Schloss, P.D. and S.L. Westcott. 2011. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl. Environ. Microbiol. 77:3219-3226. crossref(new window)

52.
Scholz, M.B., C.-C. Lo, and P.S.G. Chain. 2012. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotech. 23:9-15. crossref(new window)

53.
Stackebrandt, E. and B.M. Goebel. 1994. A place for DNA-DNA reassociation and 16S ribosomal-RNA sequenceanalysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849. crossref(new window)

54.
Sugiyama, A., J.M. Vivanco, S.S. Jayanty, and D.K. Manter. 2010. Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms. Plant Dis. 94:1329-1335. crossref(new window)

55.
Sun, Y., Y. Cai, L. Liu, F. Yu, M.L. Farrell, W. McKendree, and W. Farmerie. 2009. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 37.

56.
Sun, Y., Y. Cai, S.M. Huse, R. Knight, W.G. Farmerie, X. Wang, and V. Mai. 2012. A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief. Bioinform. 13:107-121. crossref(new window)

57.
Suzuki, M.T. and S.J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.

58.
Torsvik, V., R. Sorheim, and J. Goksoyr. 1996. Total bacterial diversity in soil and sediment communities - A review. J. Ind. Microbiol. 17:170-178. crossref(new window)

59.
Torsvik, V. and L. Ovreas. 2002. Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. 5:240-245. crossref(new window)

60.
Tzeneva, V.A., J.F. Salles, N. Naumova, W.A. de Vos, P.J. Kuikman, J. Dolfing, and H. Smidt. 2009. Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity. Research in Microbiology. 160:89-98. crossref(new window)

61.
van der Heijden, M.G., R.D. Bardgett, and N.M. van Straalen. 2008. The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 11:296-310. crossref(new window)

62.
von Wintzingerode, F., U.B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229. crossref(new window)

63.
Wang, Q., G.M. Garrity, J.M. Tiedje, and J.R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267. crossref(new window)

64.
Watanabe, K., Y. Kodama, and S. Harayama. 2001. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J. Microbiol. Meth. 44:253-262. crossref(new window)

65.
Wright, E.S., L.S. Yilmaz, and D.R. Noguera. 2012. DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl. Environ. Microbiol. 78:717-725. crossref(new window)

66.
Wu, G.D., J.D. Lewis, C. Hoffmann, Y.Y. Chen, R. Knight, K. Bittinger, J. Hwang, J. Chen, R. Berkowsky, L. Nessel, H.Z. Li, and F.D. Bushman. 2010a. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 10:206. crossref(new window)

67.
Wu, J.Y., X.T. Jiang, Y.X. Jiang, S.Y. Lu, F. Zou, and H.W. Zhou. 2010b. Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method. BMC Microbiol. 10:255. crossref(new window)

68.
Yoo, K., J. Lee, and J. Park. 2009. A review on the current methods for extracting DNA from soil and sediment environmental samples. J. Soil Groundwater Env. 14:57-67.

69.
Zhou, H.W., D.F. Li, N.F.Y. Tam, X.T. Jiang, H. Zhang, H.F. Sheng, J. Qin, X. Liu, and F. Zou. 2011. BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J. 5:741-749. crossref(new window)