Actinobacterial community structure in soils receiving long-term organic and inorganic amendments

Applied and Environmental Microbiology

Volumn 74, Issue 2, 2008, Pages 526-530

  Piao, Zhe ^a,c   Yang, Linzhang ^a   Zhao, Liping ^b   Yin, Shixue ^a,c  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b SHANGHAI JIAO TONG UNIVERSITY   (China)

^c YANGZHOU UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DENATURATION; ELECTROPHORESIS;

ACTINOBACTERIAL COMMUNITIES; CLONE LIBRARIES; DENATURING GRADIENT GEL ELECTROPHORESIS; PHYLOGENETIC DIVERSITY;

SOILS;

RIBOSOME RNA; RNA 16S;

BACTERIUM; COMMUNITY STRUCTURE; ELECTROKINESIS; MICROBIAL COMMUNITY;

ACTINOBACTERIA; ARTICLE; BIODIVERSITY; COMMUNITY STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA LIBRARY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SOIL MICROFLORA; STATISTICAL SIGNIFICANCE;

ACTINOBACTERIA; ECOSYSTEM; ELECTROPHORESIS; FERTILIZERS; MANURE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

ACTINOBACTERIA;

EID: 38349119683     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00843-07     Document Type: Article

References (29)

1. Allgaier, M., and H.-P. Grossart. 2006. Diversity and seasonal dynamics of Actinobacteria populations in four lakes in northeastern Germany. Appl. Environ. Microbiol. 72:3489-3497.
2. Ashelford, K. E., N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol. 72:5734-5741.
3. Bull, A. T., J. E. Stach, A. C. Ward, and M. Goodfellow. 2005. Marine actinobacteria: perspectives, challenges, future directions. Antonie van Leeuwenhoek 87:65-79.
4. Cao, Z. H., J. L. Ding, Z. Y. Hu, H. Knicker, I. Kogel-Knabner, L. Z. Yang, R. Yin, X. G. Lin, and Y. H. Dong. 2006. Ancient paddy soils from the Neolithic age in China's Yangtze River Delta. Naturwissenschaften 93:232-236.
5. Ellis, E. C., and S. M. Wang. 1997. Sustainable traditional agriculture in the Tai Lake region of China. Agric. Ecosyst. Environ. 61:177-193.
6. Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1:47-50.
7. Felske, A., H. Rheims, A. Wolterink, E. Stackebrandt, and A. D. Akkermans. 1997. Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiology 143:2983-2989.
8. Getha, K., S. Vikineswary, W. H. Wong, T. Seki, A. Ward, and M. Goodfellow. 2005. Evaluation of Streptomyces sp. strain g10 for suppression of Fusarium wilt and rhizosphere colonization in pot-grown banana plantlets. J. Ind. Microbiol. Biotechnol. 32:24-32.
9. Gremion, F., A. Chatzinotas, and H. Harms. 2003. Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Environ. Microbiol. 5:896-907.
10. Janssen, P. H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72:1719-1728.
11. Kemp, P. F., and J. Y. Aller. 2004. Estimating prokaryotic diversity: when are 16S rDNA libraries large enough? Limnol. Oceanogr. Methods 2:114-125.
12. Kumar, S., K. Tamura, and N. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
13. Liu, B. B., F. Zhang, X. X. Feng, Y. D. Liu, X. Yan, X. J. Zhang, L. H. Wang, and L. P. Zhao. 2006. Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison. FEMS Microbiol. Ecol. 55:274-286.
14. Loria, R., J. Kers, and M. Joshi. 2006. Evolution of plant pathogenicity in Streptomyces. Annu. Rev. Phytopathol. 44:469-487.
15. Maldonado, L. A., J. E. Stach, W. Pathom-aree, A. C. Ward, A. T. Bull, and M. Goodfellow. 2005. Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie van Leeuwenhoek 87:11-18.
16. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:695-700.
17. Nakatsu, C. H., N. Carmosini, B. Baldwin, F. Beasley, P. Kourtev, and A. Konopka. 2005. Soil microbial community responses to additions of organic carbon substrates and heavy metals (Pb and Cr). Appl. Environ. Microbiol. 71:7679-7689.
18. Nielsen, J. L., C. Klausen, P. H. Nielsen, M. Burford, and N. O. Jorgensen. 2006. Detection of activity among uncultured Actinobacteria in a drinking water reservoir. FEMS Microbiol. Ecol. 55:432-438.
19. Pawlowski, K., and A. Sirrenberg. 2003. Symbiosis between Frankia and actinorhizal plants: root nodules of non-legumes. Indian J. Exp. Biol. 41:1165-1183.
20. Rheims, H., A. Felske, S. Seufert, and E. Stackebrandt. 1999. Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments. J. Microbiol. Methods 36:65-75.
21. 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.
22. Schloss, P. D., and J. Handelsman. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl. Environ. Microbiol. 72:6773-6779.
23. Shen, M.-X., L.-Z. Yang, Y.-M. Yao, D.-D. Wu, J. Wang, R. Guo, and S. Yin. 2007. Long-term effects of fertilizer managements on crop yields and organic carbon storage of a typical rice-wheat agroecosystem of China. Biol. Fertil. Soils 44:187-200.
24. Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. B. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4374-4376.
25. Stach, J. E., and A. T. Bull. 2005. Estimating and comparing the diversity of marine actinobacteria. Antonie van Leeuwenhoek 87:3-9.
26. Stach, J. E. M., L. A. Maldonado, A. C. Ward, M. Goodfellow, and A. T. Bull. 2003. New primers for the class Actinobacteria: application to marine and terrestrial environments. Environ. Microbiol. 5:828-841.
27. Thirup, L., A. Johansen, and A. Winding. 2003. Microbial succession in the rhizosphere of live and decomposing barley roots as affected by the antagonistic strain Pseudomonas fluorescens DR54-BN14 or the fungicide imazalil. FEMS Microbiol. Ecol. 43:383-392.
28. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
29. Ward, A. C., and N. Bora. 2006. Diversity and biogeography of marine actinobacteria. Curr. Opin. Microbiol. 9:279-286.