Influence of plant polymers on the distribution and cultivation of bacteria in the phylum acidobacteria

Applied and Environmental Microbiology

Volumn 77, Issue 2, 2011, Pages 586-596

  Eichorst, Stephanie A ^a   Kuske, Cheryl R ^a   Schmidt, Thomas M ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b Michigan State University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; AGRICULTURAL SOILS; CARBON CONTENT; ENERGY SOURCE; GRASSLAND SOILS; HETEROTROPHIC BACTERIAS; HETEROTROPHS; METABOLIC CHARACTERISTICS; MICHIGAN; ORGANIC RESOURCES; PH OPTIMA; PLANT POLYMERS; SOLE CARBON;

BACTERIOLOGY; BIOPOLYMERS; DELIGNIFICATION; GENE ENCODING; OXYGEN; POLYMERS; RNA; SOILS;

CULTIVATION;

BACTERIAL DNA; POLYMER; RIBOSOME DNA; RNA 16S;

ABUNDANCE; AGRICULTURAL SOIL; BACTERIUM; GENETIC ANALYSIS; GRASSLAND SOIL; HETEROTROPHY; PHYTOCHEMISTRY; POLYMER; SOIL CARBON; SOIL MICROORGANISM; SPATIAL DISTRIBUTION;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; UNITED STATES;

BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; MICHIGAN; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANTS; POLYMERS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

MICHIGAN; UNITED STATES;

ACIDOBACTERIA; ACIDOPHILES; OPITUTACEAE; VERRUCOMICROBIA SUBDIVISION 3; VERRUCOMICROBIACEAE;

EID: 79551492681     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01080-10     Document Type: Article

References (81)

1. Alami, Y., W. Achouak, C. Marol, and T. Heulin. 2000. Rhizosphere soil aggregation and plant growth promotion of sunflowers by an exopolysaccharide- producing Rhizobium sp. strain isolated from sunflower roots. Appl. Environ. Microbiol. 66:3393-3398.
2. Alvarez, R., R. A. Diaz, N. Barbero, O. J. Santanatoglia, and L. Blotta. 1995. Soil organic carbon, microbial biomass and CO2-C production from three tillage systems. Soil Till. Res. 33:17-28.
3. Amellal, N., G. Burtin, F. Bartoli, and T. Heulin. 1998. Colonization of wheat roots by an exopolysaccharide-producing Pantoea agglomerans strain and its effect on rhizosphere soil aggregation. Appl. Environ. Microbiol. 64:3740-3747.
4. Barns, S. M., E. C. Cain, L. Sommerville, and C. R. Kuske. 2007. Acidobacteria phylum sequences in uranium contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 73:3113-3116.
5. Barns, S. M., S. L. Takala, and C. R. Kuske. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65:1731-1737.
6. Brady, N. C., and R. R. Weil. 1999. The nature and property of soils, 12th ed. Prentice Hall, Upper Saddle River, NJ.
7. Bryant, D. A., et al. 2007. Candidatus Chloracidobacterium thermophilum: An aerobic phototrophic acidobacterium. Science 317:523-526.
8. Cole, J. R., et al. 2005. The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294-D296.
9. Costerton, J. W., et al. 1987. Bacterial biofilms in nature and disease. Annu. Rev. Microbiol. 41:435-464.
10. Crocetti, G. R., J. F. Banfield, J. Keller, P. L. Bond, and L. L. Blackall. 2002. Glycogen-accumulating organisms in laboratory-scale and full-scale wastewater treatment processes. Microbiology 148:3353-3364.
11. Davis, K. E. R., S. J. Joseph, and P. H. Janssen. 2005. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl. Environ. Microbiol. 71:826-834.
12. Dedysh, S. N., T. A. Pankratov, S. E. Belova, I. S. Kulichevskaya, and W. Liesack. 2006. Phylogenetic analysis and in situ identification of bacteria community composition in an acidic sphagnum peat bog. Appl. Environ. Microbiol. 72:2110-2117.
13. Diaby, N., et al. 2007. Microbial communities in a porphyry copper tailings impoundment and their impact on the geochemical dynamics of the mine waste. Environ. Microbiol. 9:298-307.
14. Dunbar, J., S. Takala, S. M. Barns, J. A. Davis, and C. R. Kuske. 1999. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65:1662-1669.
15. Eichorst, S. A., J. A. Breznak, and T. M. Schmidt. 2007. Isolation and characterization of newly isolated soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol. 73:2708-2717.
16. Fierer, N., M. A. Bradford, and R. B. Jackson. 2007. Towards an ecological classification of soil bacteria. Ecology 88:1354-1364.
17. Fukunaga, Y., M. Kurahashi, K. Yanagi, A. Yokota, and S. Harayama. 2008. Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum "Acidobacteria." Int. J. Syst. Evol. Microbiol. 58:2597-2601.
18. Griffiths, B. S., K. Ritz, N. Ebblewhite, and G. Dobson. 1998. Soil microbial community structure: Effects of substrate loading rates. Soil Biol. Biochem. 31:145-153.
19. Hobel, C. F. V., V. T. Marteinsson, G. O. Hreggvidsson, and J. K. Kristjansson. 2005. Investigation of the microbial ecology of intertidal hot springs by using diversity analysis of 16S rRNA and chitinase genes. Appl. Environ. Microbiol. 71:2771-2776.
20. Hoejberg, O., N. P. Revsbach, and J. M. Tiedje. 1994. Denitrification in soil aggregates analyzed with microsensors for nitrous oxide and oxygen. Soil Sci. Soc. Am. J. 58:1691-1698.
21. Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
22. 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.
23. Janssen, P. H., P. S. Yates, B. E. Grinton, P. M. Taylor, and M. Sait. 2002. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl. Environ. Microbiol. 68:2391-2396.
24. Joseph, S. J., P. Hugenholtz, P. Sangwan, C. A. Osborne, and P. H. Janssen. 2003. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69:7210-7215.
25. Kim, K. S., T. G. Lilburn, M. J. Renner, and J. A. Breznak. 1998. arfI and arfII, two genes encoding α-L-arabinofuranosidases in Cytophaga xylanolytica. Appl. Environ. Microbiol. 64:1919-1923.
26. Kishimoto, N., Y. Kosako, and T. Tano. 1991. Acidobacterium capsulatum gen. nov., sp. nov.: An acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr. Microbiol. 22:1-7.
27. Klappenbach, J. A., J. M. Dunbar, and T. M. Schmidt. 2000. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66:1328-1333.
28. Klappenbach, J. A., P. R. Saxman, J. R. Cole, and T. M. Schmidt. 2001. rrndb: The ribosomal RNA operon copy number database. Nucleic Acids Res. 29:181-184.
29. Koch, I. H., F. Gich, P. F. Dunfield, and J. Overmann. 2008. Edaphobacter modestus gen. nov., sp. nov. and Edaphobacter aggregans sp. nov., two novel acidobacteria isolated from alpine and forest soils. Int. J. Syst. Bacteriol. 58:1114-1122.
30. Krieg, N. R., and P. S. Hoffman. 1986. Microaerophily and oxygen-toxicity. Annu. Rev. Microbiol. 40:107-130.
31. Kulichevskaya, I. S., N. E. Suzina, W. Liesack, and S. N. Dedysh. 2010. Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemoorganotroph from subdivision 3 of the Acidobacteria. Int. J. Syst. Evol. Microbiol. 60:301-306.
32. Kuske, C. R., et al. 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.
33. Lal, R. 2004. Soil carbon sequestration impacts on global climate change and food security. Science 304:1623-1627.
34. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., New York, NY.
35. Lane, D. J., et al. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. U. S. A. 82:6955-6959.
36. LaPara, T. M., C. H. Nakatsu, L. Pantea, and J. E. Alleman. 2000. Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. Appl. Environ. Microbiol. 66:3951-3959.
37. Lee, S., J. Ka, and J. Cho. 2008. Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiol. Lett. 285:263-269.
38. Lee, Z. M. P., C. Bussema III, and T. M. Schmidt. 2008. rrnDB: Documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. 37:D489-D493.
39. Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C. Tadler. 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am. Nat. 138:1315-1341.
40. Lozupone, C. A., and R. Knight. 2005. UniFrac: A new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
41. Ludwig, W., et al. 2004. ARB: A software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
42. Lynch, J. M., and J. M. Whipps. 1990. Substrate flow in the rhizosphere. Plant Soil 129:1-10.
43. Lynd, L. R., P. J. Weimer, W. H. van Zyl, and I. S. Pretorius. 2002. Microbial cellulose utilization: Fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 66:506-577.
44. Martiny, A. C., H.-J. Albrechtsen, E. Arvin, and S. Molin. 2005. Identification of bacteria in biofilm and bulk water samples from a nonchlorinated model drinking water distribution system: Detection of a large nitrite-oxidizing population associated with Nitrospira spp. Appl. Environ. Microbiol. 71:8611-8617.
45. Mesbah, M., U. Premachandran, and W. B. Whitman. 1989. Precise measurement of the G+C content of deoxyribonucleic acid of high-performance liquid chromatography. Int. J. Syst. Evol. Microbiol. 39:159-167.
46. Nogales, B., et al. 2001. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl. Environ. Microbiol. 67:1874-1884.
47. Pankratov, T. A., and S. N. Dedysh. Granulicella paludicola gen. nov., sp. nov., G. pectinivorans sp. nov., G. aggregans sp. nov. and G. rosea nov., novel acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int. J. Syst. Evol. Microbiol., in press.
48. Paul, E. A., and F. E. Clark. 1996. Soil microbiology and biochemistry. Academic Press, Inc., New York, NY.
49. Poindexter, J. S. Dimorphic prosthecate bacteria: The genera Caulobacter, Asticcacaulis, Hyphomicrobium, Pedomicrobium, Hyphomonas, and Thiodendron. In A. Balows, H. G. Trueper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.), The prokaryotes: A handbook on the biology of bacteria: Ecophysiology, isolation, identification, applications, 2nd ed., vol. 3. Springer- Verlag, New York, NY.
50. Pruesse, E., et al. 2007. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
51. Reicosky, D. C. 2003. Tillage-induced CO2 emissions and carbon sequestration: Effect of secondary tillage and compaction, p. 291-300. In L. Garcia- Torres, J. Benites, A. Martinez-Vilela, and A. Holgado-Cabrera (ed.), Conservation agriculture. Kluwer Academic Publishers, Dordrecht, Netherlands.
52. Roberson, E. B., and M. K. Firestone. 1992. Relationship between desiccation and exopolysaccharide production in a soil Pseudomonas sp. Appl. Environ. Microbiol. 58:1284-1291.
53. Robertson, G. P., D. C. Coleman, C. S. Bledsoe, and P. Sollins. 1999. Standard soil methods for long-term ecological research. Oxford University Press, New York, NY.
54. Robertson, G. P., E. A. Paul, and R. R. Harwood. 2000. Greenhouse gases in intensive agriculture: Contributions of individual gases to the radiative forcing of the atmosphere. Science 289:1922-1925.
55. Roop, R. M., R. M. Smibert, J. L. Johnson, and N. R. Krieg. 1984. Differential characteristics of catalase-positive campylobacters correlated with DNA homology groups. Can. J. Microbiol. 30:938-951.
56. Rosch, C., A. Mergel, and H. Bothe. 2002. Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl. Environ. Microbiol. 68:3818-3829.
57. Sait, M., K. E. R. Davis, and P. H. Janssen. 2006. Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl. Environ. Microbiol. 72:1852-1857.
58. Sait, M., P. Hugenholtz, and P. H. Janssen. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4:654-666.
59. Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Pinar, W. Lubitz, and S. Rolleke. 2002. Altamira cave Paleolithic paintings harbor partly unknown bacterial communities. FEMS Microbiol. Lett. 211:7-11.
60. Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Pinar, W. Lubitz, and S. Rolleke. 2002. Phylogenetic 16S rRNA analysis reveals the presence of complex and partly unknown bacterial communities in Tito Bustillo cave, Spain, and on its Palaeolithic paintings. Environ. Microbiol. 4:392-400.
61. Schabereiter-Gurtner, C., C. Saiz-Jimenez, G. Pinar, W. Lubitz, and S. Rolleke. 2004. Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonin and La Garma). FEMS Microbiol. Ecol. 47:235-247.
62. Schloss, P. D., et al. 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
63. Seeley, H. W., P. J. Vandemark, and J. J. Lee. 1995. Microbes in action, a laboratory manual of microbiology, fourth ed. W.H. Freeman and Co., New York, NY.
64. Sexstone, A. J., N. P. Revsbech, T. B. Parkin, and J. M. Tiedje. 1985. Direct measurement of oxygen profiles and denitrification rates in soil aggregates. Soil Sci. Soc. Am. J. 49:645-651.
65. Sievert, S. M., J. Kuever, and G. Muyzer. 2000. Identification of 16S ribosomal DNA-defined bacterial populations at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl. Environ. Microbiol. 66:3102-3109.
66. Smibert, R. M., and N. R. Krieg. 1994. Phenotypic characterization. In P. Gerhardt, R. G. E. Murray, W. A. Wood, and N. R. Krieg (ed.), Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC.
67. Smith, S. M., R. M. M. Abed, and F. Garcia-Pichel. 2004. Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, U. S. A. Microb. Ecol. 48:200-208.
68. So, C. M., and L. Y. Young. 1999. Isolation and characterization of a sulfatereducing bacterium that anaerobically degrades alkanes. Appl. Environ. Microbiol. 65:2969-2976.
69. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
70. Stevenson, B. S., S. A. Eichorst, J. T. Wertz, T. M. Schmidt, and J. A. Breznak. 2004. New strategies for cultivation and detection of previously uncultured microbes. Appl. Environ. Microbiol. 70:4748-4755.
71. Swofford, D. L. 2003. PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sinauer Associates, Sunderland, MA.
72. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
73. van Elsas, J. D., and K. Smalla. 1997. Methods for sampling soil microbes, p. 383-390. In C. J. Hurst, G. R. Knudsen, M. J. McInerney, L. D. Stetzenbach, and M. V. Walter (ed.), Manual of environmental microbiology. ASM Press, Washington, DC.
74. van Elsas, J. D., J. T. Trevors, and E. M. H. Wellington. 1997. Modern soil microbiology. Marcel Dekker Inc., New York, NY.
75. Ward, N. L., et al. 2009. Three genomes in the phylum Acidobacteria provide insight into their lifestyles in soils. Appl. Environ. Microbiol. 74:2046-2056.
76. White, P. M., and C. W. Rice. 2009. Tillage effects on microbial and carbon dynamics during plant residue decomposition. Soil Sci. Am. J. 73:138-145.
77. Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998. Prokaryotes: The unseen majority. Proc. Natl. Acad. Sci. U. S. A. 95:6578-6583.
78. Widdel, F., and F. Bak. 1991. Gram-negative mesophilic sulfate-reducing bacteria, p. 3352-3378. In A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer (ed.), The prokaryotes, 2nd ed., vol. 4. Springer-Verlag, New York, NY.
79. Wirth, S., and A. Ulrich. 2002. Cellulose degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil. Syst. Appl. Microb. 25:584-591.
80. Zimmermann, J., J. M. Gonzalez, and C. Saiz-Jimenez. 2006. Epilithic biofilms in Saint Callixtus Catacombs (Rome) harbour a broad spectrum of Acidobacteria. Antonie Van Leeuwenhoek 89:203-208.
81. Zimmermann, J., J. M. Gonzalez, C. Saiz-Jimenez, and W. Ludwig. 2005. Detection and phylogenetic relationships of highly diverse uncultured acidobacterial communities in Altamira Cave using 23S rRNA sequence analyses. Geomicrobiol. J. 22:379-388.