Myxobacterial community is a predominant and highly diverse bacterial group in soil niches

Environmental Microbiology Reports

Volumn 6, Issue 1, 2014, Pages 45-56

  Zhou, Xiu Wen ^a   Li, Shu Guang ^a   Li, Wei ^a   Jiang, De Ming ^a   Han, Kui ^a   Wu, Zhi Hong ^a   Li, Yue Zhong ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM; BIODIVERSITY; CHINA; CLASSIFICATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; MYXOCOCCALES; PHYLOGENY;

BACTERIA; BIODIVERSITY; CHINA; MOLECULAR SEQUENCE DATA; MYXOCOCCALES; PHYLOGENY; SOIL MICROBIOLOGY;

EID: 84892660332     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/1758-2229.12107     Document Type: Article

References (42)

1. Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.
2. Berleman, J.E., and Kirby, J.R. (2009) Deciphering the hunting strategy of a bacterial wolfpack. FEMS Microbiol Rev 33: 942-957.
3. Chase, J.M., Abrams, P.A., Grover, J.P., Diehl, S., Chesson, P., Holt, R.D., etal. (2002) The interaction between predation and competition: a review and synthesis. Ecol Lett 5: 302-315.
4. Chesson, P. (2000) Mechanism of maintenance of species diversity. Annu Rev Ecol Syst 31: 343-366.
5. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., etal. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
6. Crespi, B.J. (2001) The evolution of social behavior in microorganisms. Trends Ecol Evol 16: 178-183.
7. Dawid, W. (2000) Biology and global distribution of myxobacteria in soils. FEMS Microbiol Rev 24: 403-427.
8. Dworkin, M. (1996) Recent advances in the social and developmental biology of the myxobacteria. Microbiol Rev 60: 70-102.
9. Epstein, S.S. (2009) Uncultivated microorganisms. In Microbiology Monographs. Steinbüchel, A. (ed.). New York, USA: Springer-Verlag, pp. 121-131.
10. Fierer, N., Morse, J.L., Berthrong, S.T., Bernhardt, E.S., and Jackson, R.B. (2007) Environmental controls on the landscape-scale biogeography of stream bacterial communities. Ecology 88: 2162-2173.
11. Gans, J., Wolinsky, M., and Dunbar, J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
12. Jiang, D.M., Wu, Z.H., Zhao, J.Y., and Li, Y.Z. (2007) Fruiting and non-fruiting myxobacteria: a phylogenetic perspective of cultured and uncultured members of this group. Mol Phylogenet Evol 44: 545-552.
13. Kaiser, D. (2003) Coupling cell movement to multicellular development in myxobacteria. Nat Rev Microbiol 1: 45-54.
14. Kolton, M., Meller Harel, Y., Pasternak, Z., Graber, E.R., Elad, Y., and Cytryn, E. (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.
15. LaMontagne, M.G., Schimel, J.P., and Holden, P.A. (2003) Comparison of subsurface and surface soil bacterial communities in California grassland as assessed by terminal restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes. Microb Ecol 46: 216-227.
16. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematic. Stackebrandt, E., and Goodfellow, M. (eds). New York, USA: John Wiley and Sons, pp. 115-175.
17. Lauber, C.L., Hamady, M., Knight, R., and Fierer, N. (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.
18. Lueders, T., Kindler, R., Miltner, A., Friedrich, M.W., and Kaestner, M. (2006) Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microbiol 72: 5342-5348.
19. 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.
20. Miller, M.B., and Bassler, B.L. (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55: 165-199.
21. Muyzer, G., de Waal, E.C., and Uitterlinden, A.G. (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.
22. Nacke, H., Thurmer, A., Wollherr, A., Will, C., Hodac, L., Herold, N., etal. (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS ONE 6: e17000.
23. Nossa, C.W., Oberdorf, W.E., Yang, L., Aas, J.A., Paster, B.J., Desantis, T.Z., etal. (2010) Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol 16: 4135-4144.
24. O'Connor, K.A., and Zusman, D.R. (1988) Reexamination of the role of autolysis in the development of Myxococcus xanthus. J Bacteriol 170: 4103-4112.
25. Pfaffl, M.W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.
26. Reichenbach, H. (1999) The ecology of the myxobacteria. Environ Microbiol 1: 15-21.
27. Reichenbach, H. (2004) The Myxococcales. In Bergey's Manual of Systematic Bacteriology. Garrity, G.M. (ed.). New York, USA: Springer-Verlag, pp. 1059-1143.
28. Roesch, L.F., Fulthorpe, R.R., Riva, A., Casella, G., Hadwin, A.K., Kent, A.D., etal. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1: 283-290.
29. Rosenberg, E., Keller, K.H., and Dworkin, M. (1977) Cell density-dependent growth of Myxococcus xanthus on casein. J Bacteriol 129: 770-777.
30. Schloss, P.D., and Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
31. Schloss, P.D., and Handelsman, J. (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2: e92.
32. 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.
33. Shimkets, L., Dworkin, M., and Reichenbach, H. (2006) The myxobacteria. In The Prokaryotes, 3rd edn, Vol. 7. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.H., and Stackebrandt, E. (eds). Heidelberg, Germany: Springer, pp. 31-115.
34. Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
35. Turner, S., Pryer, K.M., Miao, V.P., and Palmer, J.D. (1999) Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 46: 327-338.
36. Uroz, S., Buée, M., Murat, C., Frey-Klett, P., and Martin, F. (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2: 281-288.
37. Whitman, W.B., Coleman, D.C., and Wiebe, W.J. (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95: 6578-6583.
38. Will, C., Thurmer, A., Wollherr, A., Nacke, H., Herold, N., Schrumpf, M., etal. (2010) Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76: 6751-6759.
39. Wireman, J.W., and Dworkin, M. (1977) Developmentally induced autolysis during fruiting body formation by Myxococcus xanthus. J Bacteriol 129: 798-802.
40. Wu, Z.H., Jiang, D.M., Li, P., and Li, Y.Z. (2005) Exploring the diversity of myxobacteria in a soil niche by myxobacteria-specific primers and probes. Environ Microbiol 7: 1602-1610.
41. Zhang, H., Dong, H., Zhao, J., Hu, W., and Li, Y.Z. (2005) Characterization of developmental autolysis in myxobacterial fruiting body morphogenesis with profiling of amino acids using capillary electrophoresis method. Amino Acids 28: 319-325.
42. Zhou, J., Xia, B., Treves, D.S., Wu, L.Y., Marsh, T.L., O'Neill, R.V., etal. (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68: 326-334.