Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream

Applied and Environmental Microbiology

Volumn 73, Issue 3, 2007, Pages 756-767

  Das, Mitali ^a   Royer, Todd V ^b   Leff, Laura G ^a  

^a KENT STATE UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOFILMS; BIOMASS; DECOMPOSITION; ECOSYSTEMS; ELECTROPHORESIS; FUNGI; RIVERS;

ACTINOMYCETES; LEAVES; PCR-DENATURING GRADIENT GEL ELECTROPHORESIS (DGGE); RIBOTYPE RICHNESS;

BIODIVERSITY;

BACTERIUM; BIOMASS; COMMUNITY STRUCTURE; DNA; FUNGUS; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY; SPECIES RICHNESS; STREAM;

ACTINOBACTERIA; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GROWTH; BIOFILM; BIOMASS; COMMUNITY STRUCTURE; DECOMPOSITION; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA EXTRACTION; FUNGUS GROWTH; MICROFLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; OAK; PLANT LEAF; POLYMERASE CHAIN REACTION; RIBOTYPING; SPECIES HABITAT; STATISTICAL SIGNIFICANCE; STREAM (RIVER); SUGAR MAPLE; UNITED STATES;

ACER; ACTINOBACTERIA; BACTERIA; DNA, BACTERIAL; DNA, FUNGAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FUNGI; PLANT LEAVES; POLYMERASE CHAIN REACTION; QUERCUS; RIVERS; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S;

NORTH AMERICA; OHIO; UNITED STATES;

ACER SACCHARUM; ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); FUNGI; QUERCUS ALBA;

EID: 33846938747     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01170-06     Document Type: Article

References (73)

1. Baldy, V., E. Chauvet, and M. O. Gessner. 1995. Bacteria, fungi and the breakdown of leaf litter in a large river. Oikos 74:93-102.
2. Baldy, V., E. Chauvet, J. Y. Charcosset, and M. O. Gessner. 2002. Microbial dynamics associated with leaves decomposing in the mainstem and floodplain of a large river. Aquat. Microbiol. Ecol. 28:25-36.
3. Bärlocher, F., and B. Kendrick. 1974. Dynamics of fungal populations on leaves in a stream. J. Ecol. 62:761-791.
4. Bärlocher, F. 1985. The role of fungi in the nutrition of stream invertebrates. Bot. J. Linn. Soc. 91:83-94.
5. Blackwood, C. B., T. Marsh, S.-H. Kim, and E. A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl. Environ. Microbiol. 69:926-932.
6. Boon, N., W. De Windt, W. Verstraete, and E. M. Top. 2002. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol. Ecol. 39:101-112.
7. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
8. Buchan, A., S. Y. Newell, M. Butler, E. J. Biers, J. T. Hollibaugh, and M. A. Moran. 2003. Dynamics of bacterial and fungal communities on decaying salt marsh grass. Appl. Environ. Microbiol. 69:6676-6687.
9. Chamier, A. C. 1985. Cell-wall degrading enzymes of aquatic hyphomycetes: a review. Bot. J. Linnean Soc. 91:67-81.
10. Daniel, G. F., T. Nilsson, and A. P. Singh. 1987. Degradation of lignocellulosics by unique tunnel-forming bacteria. Can. J. Microbiol. 33:943-948.
11. Das, M. 2006. Microbial community structure and interactions in leaf litter in a stream. Ph.D. dissertation. Kent State University, Kent, Ohio.
12. Embley, T. M., and E. Stackebrandt. 1994. The molecular phylogeny and systematics of the actinomycetes. Annu. Rev. Microbiol. 48:257-289.
13. Ferris, M. J., G. Muyzer, and D. M. Ward. 1990. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 62:340-346.
14. Findlay, S., J. Tank, S. Dye, H. M. Valett, P. J. Mulholland, W. H. McDowell, S. L. Johnson, S. K. Hamilton, J. Edmonds, W. K. Dodds, and W. B. Bowden. 2002. A cross-system comparison of bacterial and fungal biomass in detrital pools of headwater streams. Microb. Ecol. 43:55-66.
15. Fisher, S. G., and G. E. Likens. 1973. Energy flow in Bear Brook, New Hampshire: an integrative approach to stream ecosystem metabolism. Ecol. Monogr. 43:421-439.
16. Fromin, N., J. Hamelin, S. Tarnawski, D. Roesti, K. Jourdain-Miserez, B. Forestier, S. Teyssier-Cuvelle, F. Gillet, M. Aragno, and P. Rossi. 2002. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ. Microbiol. 4:634-643.
17. Gessner, M. O., and E. Chauvet. 1993. Ergosterol-to-biomass conversion factors for aquatic hyphomycetes. Appl. Environ. Microbiol. 59:502-507.
18. Gessner, M. O., and S. Y. Newell. 2002. Biomass, growth rate, and production of filamentous fungi in plant litter, p. 390-408. In C. J. Hurst, R. L. Crawford, G. Knudsen, M. McInerney, and L. D. Stetzenbach (ed.), Manual of environmental microbiology, 2nd ed. American Society for Microbiology, Washington, DC.
19. Goh, T. K., and K. D. Hyde. 1996. Biodiversity of freshwater fungi. J. Ind. Microbiol. 17:328-345.
20. Griffiths, R. I., A. S. Whiteley, A. G. O'Donnell, and M. J. Bailey. 2003. Influence of depth and sampling time on bacterial community structure. FEMS Microbiol. Ecol. 43:35-43.
21. Gulis, V., and K. Suberkropp. 2003. Effect of inorganic nutrients on relative contributions of fungi and bacteria to carbon flow from submerged decomposing leaf litter. Microb. Ecol. 45:11-19.
22. Heuer, H., M. Krsek, P. Baker, K. Smalla, and E. M. H. Wellington. 1997. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:3233-3241.
23. Hieber, M., and M. O. Gessner. 2002. Contribution of stream detritivores, fungi and bacteria to leaf breakdown based on biomass estimates. Ecology 83:1026-1038.
24. Ibekwe, A. M., S. K. Papiernik, J. Gan, S. R. Yates, C.-H. Yang, and D. E. Crowley. 2001. Impact of fumigants on soil microbial communities. Appl. Environ. Microbiol. 67:3245-3257.
25. Kaushik, N. K., and H. B. N. Hynes. 1971. The fate of dead leaves that fall into streams. Arch. Hydrobiol. 68:465-515.
26. Loferer-Krößbacher, M., J. Kilma, and R. Psenner. 1998. Determination of bacterial cell dry mass by transmission electron microscopy and densitometric image analysis. Appl. Environ. Microbiol. 64:688-694.
27. Lydell, C., L. Dowell, M. Sikaroodi, P. Gillevet, and D. Emerson. 2004. A population survey of the members of the phylum Bacteroidetes isolated from salt marsh sediments along the east coast of the United States. Microb. Ecol. 48:263-273.
28. Maamri, A., F. Bärlocher, E. Pattee, and H. Chergui. 2001. Fungal and bacterial colonization of Salix pedicellata leaves decaying in permanent and intermittent streams in Eastern Morocco. Int. Rev. Hydrobiol. 86:337-348.
29. May, L. A., B. Smiley, and M. G. Schmidt. 2001. Comparative denaturing gradient gel electrophoresis of fungal communities associated with whole plant corn silage. Can. J. Microbiol. 47:829-841.
30. McCaig, A. E., L. A. Glover, and J. I. Prosser. 2001. Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl. Environ. Microbiol. 67:4554-4559.
31. McCarthy, A. J. 1987. Lignocellulose-degrading actinomycetes. FEMS Microbiol. Rev. 46:145-163.
32. McNamara, C. J., M. J. Lemke, and L. G. Leff. 2002. Culturable and non-culturable fractions of bacterial populations in sediments of a South Carolina stream. Hydrobiologia 482:151-159.
33. McNamara, C. J., and L. G. Leff. 2004. Bacterial community composition in biofilms on leaves in a northeastern Ohio stream. J. N. Am. Benthol. Soc. 23:677-685.
34. Meyer, J. L., and C. Johnson. 1983. The influence of elevated nitrate concentration on rate of leaf decomposition in a stream. Freshwater Biol. 13:177-183.
35. Mille-Lindblom, C., and L. J. Tranvik. 2003. Antagonism between bacteria and fungi on decomposing aquatic plant litter. Microb. Ecol. 45:173-182.
36. Minshall, G. W. 1967. Role of allochthonous detritus in the trophic structure of an alpine springbrook community. Ecology 48:139-149.
37. Mullis, K. B., and F. A. Faloona. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155:335-350.
38. 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.
39. Muyzer, G., and E. C. de Waal. 1994. Determination of the genetic diversity of microbial communities using DGGE analysis of PCR-amplified 16S rRNA. NATO ASI Ser. G 35:207-214.
40. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
41. Muyzer, G., and K. Smalla. 1998. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek 73:127-141.
42. Nikolcheva, L. G., A. M. Cockshutt, and F. Bärlocher. 2003. Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches. Appl. Environ. Microbiol. 69:2548-2554.
43. Nikolcheva, L. G., and F. Bārlocher. 2004. Taxon-specific fungal primers reveal unexpectedly high diversity during leaf decomposition in a stream. Mycol. Prog. 3:41-49.
44. Nikolcheva, L. G., and F. Bärlocher. 2005. Seasonal and substrate preferences of fungi colonizing leaves in streams: traditional versus molecular evidence. Environ. Microbiol. 7:270-280.
45. Nübel, U., B. Engelen, A. Felske, J. Snaidr, A. Weishuber, R. I. Amman, W. Ludwig, and W. Backhaus. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:5636-5643.
46. Nübel, U., F. Garcia-Pichel, M. Kühl, and G. Muyzer. 1999. Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol. 65:422-430.
47. Ostrofsky, M. L. 1997. Relationship between chemical characteristics of autumn-shed leaves and aquatic processing rates. J. N. Am. Benthol. 16:750-759.
48. Otoguro, M., M. Hayakawa, T. Yamazaki, and Y. Iimura. 2001. An integrated method for the enrichment and selective isolation of Actinokineospora spp. in soil and plant litter. J. Appl. Microbiol. 91:118-130.
49. Porter, D., S. Y. Newell, and W. L. Lingle. 1989. Tunneling bacteria in decaying leaves of a seagrass. Aquat. Bot. 35:395-401.
50. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceangr. 25:943-948.
51. Posch, T., M. Loferer-Krössbacher, G. Gao, A. Alfreider, J. Pernthaler, and R. Psenner. 2001. Precision of bacterioplankton biomass determination: a comparison of two fluorescent dyes, and of allometric and linear volume-to-carbon conversion factors. Aquat. Microb. Ecol. 25:55-63.
52. Reche, I., E. Pulido-Villena, R. Moraes-Baquero, and E. O. Casamayor. 2005. Does ecosystem size determine aquatic bacterial richness? Ecology 86:1715-1722.
53. Rowe, J. M., S. K. Meegan, E. S. Engstrom, S. A. Perry, and W. B. Perry. 1996. Comparison of leaf processing rates under different temperature regimes in three headwater streams. Freshwater Biol. 36:277-288.
54. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239:487-491.
55. Schäfer, H., and G. Muyzer. 2001. Denaturing gradient gel electrophoresis in marine microbial ecology. Methods Microbiol. 30:425-468.
56. Shearer, C. A. 1992. The role of woody debris, p. 77-98. In F. Bärlocher (ed.), The ecology of aquatic hyphomycetes. Springer-Verlag, Berlin, Germany.
57. Sinsabaugh, R. L., and A. E. Linkins. 1990. Enzymatic and chemical analysis of particulate organic matter from a boreal river. Freshwater Biol. 23:301-309.
58. Smalla, K., N. Cresswell, L. C. Mendoca-Hagler, A. Wolters, and J. D. van Elsas. 1993. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:78-85.
59. Srinivasan, M. C., R. S. Laxman, and M. V. Deshpande. 1991. Physiology and nutrition aspects of actinomycetes - an overview. World J. Microbiol. Biotechnol. 7:171-184.
60. Sterflinger, K., W. E. Krumbein, and A. Schwiertz. 1998. A protocol for PCR in situ hybridization of hyphomycetes. Int. Microbiol. 1:217-220.
61. Suberkropp, K. 1992. Interactions with invertebrates, p. 118-134. In F. Bärlocher (ed.), The ecology of aquatic hyphomycetes. Springer-Verlag, Berlin, Germany.
62. Suberkropp, K. 1998. Effects of dissolved nutrients on aquatic hyphomycetes growing on leaf litter. Mycol. Res. 102:998-1002.
63. Suberkropp, K., and M. J. Klug. 1976. Fungi and bacteria associated with leaves during processing in a woodland stream. Ecology 57:707-719.
64. Suberkropp, K., and E. Chauvet. 1995. Regulation of leaf breakdown in streams: influences of water chemistry. Ecology 76:1433-1445.
65. Tamura, T., M. Hayakawa, H. Nonomura, A. Yokota, and K. Hatano. 1995. Four new species of the genus Actinokineospora: Actinokineospora inagensis sp. nov., Actinokineospora globicatena sp. nov., Actinokineospora terrae sp. nov., and Actinokineospora diospyrosa sp. nov. Int. J. Syst. Bacteriol. 45:371-378.
66. Tank, J. L., and J. R. Webster. 1998. Interaction of substrate and nutrient availability on wood biofilm processes in streams. Ecology 79:2168-2179.
67. van Dillewijn, P., P. J. Villadas, and N. Toro. 2002. Effect of a Sinorhizobium meliloti strain with a modified putA gene on the rhizosphere microbial community of alfalfa. Appl. Environ. Microbiol. 68:4201-4208.
68. van Hannen, E. J., G. Zwart, M. P. van Agterveld, J. Gons, J. Ebert, and H. J. Laanbroek. 1999. Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl. Environ. Microbiol. 65:795-801.
69. Vicuña, R. 1988. Bacterial degradation of lignin. Enzyme Microbiol. Technol. 10:646-656.
70. Weyers, H. S., and K. Suberkropp. 1996. Fungal and bacterial production during leaf breakdown of yellow poplar leaves in two streams. J. N. Am. Benthol. Soc. 15:408-420.
71. White, T. J., T. Bruns, S. Lee, and J. W. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p. 315-322. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR protocols: a guide to methods and applications. Academic Press, Inc., New York, NY.
72. Willoughby, L. G. 1974. Decomposition of litter in freshwater, p. 659-681. In C. H. Dickinson and J. F. Pugh (ed.), Biology of plant litter decomposition. Academic Press, London, United Kingdom.
73. Wohl, D., and J. V. McArthur. 1998. Actinomycete-flora associated with submersed freshwater macrophytes. FEMS Microbiol. Ecol. 26:135-140.