Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use

Soil Biology and Biochemistry

Volumn 40, Issue 11, 2008, Pages 2762-2770

  Acosta Martinez V ^a   Dowd, S ^a   Sun, Y ^b   Allen, V ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b Medical Biofilm Research Institute Lubbock   (United States)

^c TEXAS TECH UNIVERSITY   (United States)

Author keywords

454 Pyrosequencing; Bacterial diversity; Conservation Reserve Program; Cotton; Integrated crop livestock production; Land use; Soil management

Indexed keywords

AGRICULTURAL PRODUCTS; BACTERIOLOGY; BIOMASS; CHROMIUM; CLAY MINERALS; COTTON; LAND USE; MANAGEMENT; RENEWABLE ENERGY RESOURCES; ROTATION;

454 PYROSEQUENCING; BACTERIAL DIVERSITY; CONSERVATION RESERVE PROGRAM; INTEGRATED CROP-LIVESTOCK PRODUCTION; SOIL MANAGEMENT;

SOILS;

ABUNDANCE; BACTERIUM; CONSERVATION PLANNING; COTTON; GRASS; HUMAN ACTIVITY; LAND USE CHANGE; LIVESTOCK FARMING; MONOCULTURE; SOIL MANAGEMENT; SOIL MICROORGANISM; SOIL TYPE; SPECIES DIVERSITY; WHEAT;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); BOTHRIOCHLOA BLADHII; GOSSYPIUM HIRSUTUM; POACEAE; TRITICUM AESTIVUM; ZEA MAYS;

EID: 53449086190     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2008.07.022     Document Type: Article

References (45)

1. Abell G.C.J., and Bowman J.P. Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater. FEMS Microbiology Ecology 53 (2005) 379-391
2. Acosta-Martínez V., Zobeck T.M., and Allen V.G. Soil microbial, chemical and physical properties in continuous cotton and integrated crop-livestock systems. Soil Science Society America Journal 68 (2004) 1875-1884
3. Acosta-Martínez, V., Burow, G., Allen, V.G., Soil microbial community structure, diversity and functionality in continuous cotton compared to alternative systems. Soil Science Society America Journal, submitted for publication.
4. Allen V.G., Brown C.P., Segarra E., Green C.J., Wheeler T.A., Acosta-Martinez V., and Zobeck T.M. In search of sustainable agricultural systems for the Llano Estacado of the U.S. Southern High Plains. Agriculture, Ecosystems and Environment 12 (2007) 3-12
5. Altschul S.F., Gish W., and Miller W. Basic local alignment search tool. Journal Molecular Biology 215 (1990) 403-410
6. Brookes P.C., Landman A., Pruden G., and Jenkinson D.S. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biology and Biochemistry 17 (1985) 837-842
7. Chan O.C., Casper P., Qing S.L., Li F.Z., Fu Y., Dong Y.X., Ulrich A., and Ming Z.X. Vegetation cover of forest, shrub and pasture strongly influences soil bacterial community structure as revealed by 16S rRNA gene T-RFLP analysis. FEMS Microbiology Ecology 64 (2008) 449-458
8. Chao A., and Bunge J. Estimating the number of species in a stochastic abundance model. Biometrics 58 (2002) 531-539
9. Cole J.R., Chai B., Farris R.J., Wang Q., Kulam-Syed-Mohideen A.S., McGarrell D.M., Bandela A.M., Cardenas E., Garrity G.M., and Tiedje J.M. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Research 35 (2007) D169-D172
10. Cristea-Fernstrom M., Olofsson M., and Chryssanthou E. Pyrosequencing of a short hypervariable 16S rDNA fragment for the identification of nontuberculous mycobacteria-a comparison with conventional 16S rDNA sequencing and phenotyping. Acta Pathologica Microbiologica et Immunologica Scandinavica 115 (2007) 1252-1259
11. DeSantis T.Z., Hugenholtz P., Larsen N., Rojas M., Brodie E.L., Keller K., Huber T., Dalevi D., Hu P., and Andersen G.L. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology 72 (2006) 5069-5072
12. Dowd S.E., Zaragoza J., Rodriguez J.R., Oliver M.J., and Payton P.R. Windows.NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). BMC Bioinformatics 6 (2005) 93
13. Dowd S.E., Callaway T.R., Wallcott R.D., Sun Y., McKeehan T., Hagevoort R.G., and Edrington T.S. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Microbiology 8 (2008) 125
14. Dowd, S.E., Sun, Y., Wolcott, R.D., Carroll, J.A., 2008b. Novel bacterial diagnostic and microbiome evaluation tool. Foodborne Pathogens and Disease, in press.
15. Drijber R.A., Doran J.W., Parkhurst A.M., and Lyon D.J. Changes in soil microbial community structure with tillage under long-term wheat-fallow management. Soil Biology and Biochemistry 32 (2000) 1419-1430
16. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32 (2004) 1792-1797
17. Farrelly V., Rainey F.A., and Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Applied and Environmental Microbiology 61 (1995) 2798-2801
18. Felsenstein J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5 (1989) 164-166
19. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6. Distributed by the author (2005), Department of Genome Sciences, University of Washington, Seattle
20. Gans J., Wolinsky M., and Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309 (2005) 1387-1389
21. Jenkinson D.S. Determination of microbial biomass carbon and nitrogen in soil. In: Wilson J.R. (Ed). Advances in Nitrogen Cycling in Agricultural Ecosystems, CAB Int., Walling-ford, UK (1988), Marcel Dekker, New York 368-386
22. Huang X., and Madan A. CAP3: a DNA sequence assembly program. Genome Research 9 (1999) 868-877
23. Huse S.M., Huber J.A., and Morrison H.G. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8 (2007) R143
24. Kennedy A.C. Microbial diversity in agroecosystem quality. In: Collins W.W., and Qualset C.O. (Eds). Biodiversity in Agroecosystems (1999), CRC Press, Boca Raton, FL 1-17
25. Kennedy A.C., and Schillinger W.F. Soil quality and water intake in traditional-till vs. no-till paired farms in Washington's Palouse region. Soil Science Society of America Journal 70 (2006) 940-949
26. Liu Z., Lozupone C., and Hamady M. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Research 35 (2007) e120
27. Lynch J.M., and Bragg E. Microorganisms and soil aggregate stability. Advances in Soil Sciences 2 (1985) 133-171
28. Maidak B.L., Cole J.R., Lilburn T.G., Parker Jr. C.T., Saxman P.R., Farris R.J., Garrity G.M., Olsen G.J., Schmidt T.M., and Tiedje J.M. The RDP-II (Ribosomal Database Project). Nucleic Acids Research 29 (2001) 173-174
29. Margalef R. Information theory in ecology. General Systematics 3 (1958) 36-71
30. NCSS. NCSS User's Guide, Version 7.1 (2007), Kaysville, Utah
31. Nocker A., Burr M., and Camper A.K. Genotypic microbial community profiling: a critical technical review. Microbial Ecology 54 (2007) 276-289
32. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome 11 (2001) 3-11
33. Roesch L.F., Fulthrope R.R., Riva A., Casella G., Hadwin A.K.M., Kent A.D., Daroub S.M., Camargo F.A.O., Farmerie W.G., and Triplett E.W. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal 1 (2007) 283-290
34. SAS Institute. SAS/STAT User's Guide, Version 9.1.3 (2002), The SAS Institute, Cary, NC
35. Schloss P.D., and Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 71 (2005) 1501-1506
36. Seber G.A.F., and Wild C.J. Nonlinear Regression (1989), John Wiley & Sons, New York
37. Sundquist A., Bigdeli S., Jalili R., Druzin M.L., Waller S., Pullen K.M., El-Sayed Y.Y., Taslimi M.M., Batzoglou S., and Ronaghi M. Bacterial flora typing with deep, targeted, chip-based Pyrosequencing. BMC Microbiology 7 (2007) 108
38. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Applied and Environmental Microbiology 62 (1996) 625-630
39. Texas Alliance for Water Conservation (TAWC). 2007. Report on an integrated approach to water conservation for agriculture in the Texas Southern High Plains. pp. 1-270. Available from: .
40. Vance E.D., Brookes P.C., and Jenkinson D.S. An extraction method for measuring microbial biomass C. Soil Biology and Biochemistry 19 (1987) 703-707
41. Vandever, M., 2007. The Conservation Reserve Program. U.S. Geological Survey, Science in Your Backyard: Texas, Biological Resource Information. Available from: .
42. Vestal J.R., and White D.C. Lipid analysis in microbial ecology. BioScience 39 (1989) 535-541
43. von W.F., Gobel U.B., and Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Review 21 (1997) 213-229
44. Weiss P., Schweitzer B., Amann R., and Simon M. Identification in situ and dynamics of bacteria on limnetic organic aggregates (Lake Snow). Applied Environmental Microbiology 62 (1996) 1998-2005
45. Wu J., Joergensen R.G., Pommerening B., Chaussod R., and Brookes P.C. Measurement of soil microbial biomass C by fumigation extraction - an autoclaved procedure. Soil Biology and Biochemistry 22 (1990) 1167-1169