Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study

Environmental Microbiology Reports

Volumn 4, Issue 2, 2012, Pages 248-256

  Steven, Blaire ^a   Gallegos Graves, La Verne ^a   Starkenburg, Shawn R ^a   Chain, Patrick S ^a   Kuske, Cheryl R ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYANOBACTERIA; LARREA TRIDENTATA;

EID: 84858613358     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2012.00328.x     Document Type: Article

References (45)

1. Ashelford, K.E., Chuzhanova, N.A., Fry, J.C., Jones, A.J., and Weightman, A.J. (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.
2. Bardgett, R.D., Freeman, C., and Ostle, N.J. (2008) Microbial contributions to climate change through carbon cycle feedbacks. ISME J 2: 805-814.
3. Belnap, J., and Gardner, J.S. (1993) Soil microstructure in soils of the Colorado Plateau - the role of the cyanobacterium Microcoleus vaginatus. Great Basin Nat 53: 40-47.
4. Belnap, J., Büdel, B., and Lange, O.L. (2001) Biological soil crusts: characteristics and distribution. In Biological Soil Crusts: Structure, Function, and Management. Belnap, J., and Lange, O.L. (eds). Berlin, Germany: Springer-Verlag, pp. 3-30.
5. 2. Glob Chang Biol 11: 203-212.
6. 2 and N fertilization. Glob Chang Biol 14: 1025-1036.
7. Büdel, B. (2001) Synopsis: comparative biogeography of soil-crust biota. In Biological Soil Crusts: Structure, Function, and Management. Belnap, J., and Lange, O.L. (eds). Berlin, Germany: Springer-Verlag, pp. 141-152.
8. Castro, H.F., Classen, A.T., Austin, E.E., Norby, R.J., and Schadt, C.W. (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76: 999-1007.
9. Chen, L.Z., Li, D.H., and Liu, Y.D. (2003) Salt tolerance of Microcoleus vaginatus Gom., a cyanobacterium isolated from desert algal crust, was enhanced by exogenous carbohydrates. J Arid Environ 55: 645-656.
10. Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam, S.A., McGarrell, D.M., etal. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: D294-D296.
11. Engelbrektson, A., Kunin, V., Wrighton, K.C., Zvenigorodsky, N., Chen, F., Ochman, H., and Hugenholtz, P. (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 4: 642-647.
12. Forney, L.J., Zhou, X., and Brown, C.J. (2004) Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7: 210-220.
13. Garcia-Pichel, F., López-Cortés, A., and Nübel, U. (2001) Phylogenetic and morphological diversity of cyanobacteria in soil desert crusts from the Colorado plateau. Appl Environ Microbiol 67: 1902-1910.
14. Gomez-Alvarez, V., Teal, T.K., and Schmidt, T.M. (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J 3: 1314-1317.
15. Huson, D.H., Auch, A.F., Qi, J., and Schuster, S.C. (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
16. Jones, R.T., Robeson, M.S., Lauber, C.L., Hamady, M., Knight, R., and Fierer, N. (2009) A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3: 442-453.
17. 2 Enrichment (FACE) Facility. Glob Chang Biol 5: 659-668.
18. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., etal. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-D484.
19. Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., and Hugenholtz, P. (2008) A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 72: 557-578.
20. Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
21. Kuske, C.R., Ticknor, L.O., Miller, M.E., Dunbar, J.M., Davis, J.A., Barns, S.M., and Belnap, J. (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68: 1854-1863.
22. Langhans, T.M., Storm, C., and Schwabe, A. (2009) Community assembly of biological soil crusts of different successional stages in a temperate sand ecosystem, as assessed by direct determination and enrichment techniques. Microb Ecol 58: 394-407.
23. Li, S., and Chou, H.H. (2004) LUCY2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics 20: 2865-2866.
24. 2 on soil microbial biomass, activity, and diversity in a chaparral ecosystem. Appl Environ Microbiol 71: 8573-8580.
25. Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., etal. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
26. Morgan, J.L., Darling, A.E., and Eisen, J.A. (2010) Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5: e10209.
27. Nagy, M.L., Perez, A., and Garcia-Pichel, F. (2005) The prokaryotic diversity of biological soil crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ). FEMS Microbiol Ecol 54: 233-245.
28. Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H.Y., Cohoon, M., etal. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
29. Parks, D.H., and Beiko, R.G. (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-721.
30. 2 and temperature: a discussion of observations, measurement methods, and models. New Phytol 162: 311-322.
31. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glockner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
32. Richter, D.C., Ott, F., Auch, A.F., Schmid, R., and Huson, D.H. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE 3: e3373.
33. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., etal. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
34. Spiegelman, D., Whissell, G., and Greer, C.W. (2005) A survey of the methods for the characterization of microbial consortia and communities. Can J Microbiol 51: 355-386.
35. Stark, M., Berger, S.A., Stamatakis, A., and von Mering, C. (2010) MLTreeMap-accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics 11: 461.
36. Starkenburg, S.R., Reitenga, K.G., Freitas, T., Johnson, S., Chain, P.S., Garcia-Pichel, F., and Kuske, C.R. (2011) The genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide. J Bacteriol 193: 4569-4570.
37. Tringe, S.G., and Hugenholtz, P. (2008) A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11: 442-446.
38. Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., etal. (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
39. Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R., and Gordon, J.I. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
40. Walker, A. (2010) A glut from the gut: metagenomics takes a giant step foward. Nat Rev Microbiol 8: 315.
41. White, J.R., Nagarajan, N., and Pop, M. (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352.
42. Yeager, C.M., Kornosky, J.L., Housman, D.C., Grote, E.E., Belnap, J., and Kuske, C.R. (2004) Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado Plateau and Chihuahuan Desert. Appl Environ Microbiol 70: 973-983.
43. 2-fixing members of biological soil crusts of the Colorado Plateau, USA. FEMS Microbiol Ecol 60: 85-97.
44. 2, fine roots and the response of soil microorganisms: a review and hypothesis. New Phytol 147: 201-222.
45. Zhang, H., DiBaise, J.K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., etal. (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 106: 2365-2370.