Temporal changes in diversity and expression patterns of fungal laccase genes within the organic horizon of a brown forest soil

Soil Biology and Biochemistry

Volumn 41, Issue 7, 2009, Pages 1380-1389

  Kellner, Harald ^a,b   Luis, Patricia ^c   Schlitt, Bettina ^a,b   Buscot, François ^a,b  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c University of Lyon   (France)

Author keywords

Ascomycetes; Basidiomycetes; Laccase gene expression; Lignin degradation

Indexed keywords

ENZYME ACTIVITY; FORESTRY; FUNGI; NUCLEIC ACIDS; RNA; SOILS; STABILIZATION;

ASCOMYCETES; BASIDIOMYCETE LACCASE; BASIDIOMYCETES; LIGNIN DEGRADATION; PHYLOGENETIC ANALYSIS; SOIL ENZYME ACTIVITY; SOIL ORGANIC MATTER TURNOVER; STABILIZATION PROCESS;

GENE EXPRESSION;

BROWN SOIL; CAMBISOL; DECIDUOUS FOREST; ENZYME ACTIVITY; FOREST SOIL; FUNGUS; GENE EXPRESSION; SPECIES DIVERSITY; TEMPORAL VARIATION;

DEGRADATION; ENZYMES; FUNGI; GENES; LACCASE; LIGNINS; NUCLEIC ACIDS; SOIL;

ASCOMYCOTA; BASIDIOMYCOTA; FAGUS;

EID: 67349261459     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2009.03.012     Document Type: Article

References (45)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25 (1997) 3389-3402
2. Aneja M.K., Sharma S., Fleischmann F., Stich S., Heller W., Bahnweg G., Munch J.C., and Schloter M. Microbial colonization of Beech and Spruce litter - influence of decomposition site and plant litter species on the diversity of microbial community. Microbial Ecology 52 (2006) 127-135
3. Baldrian P. Fungal laccases: occurrence and properties. FEMS Microbiology Reviews 30 (2006) 215-242
4. Beals E.W. Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Advances in Ecological Research 14 (1984) 1-55
5. Berg B., and Gerstberger P. Element fluxes with litterfall in mature stands of Norway Spruce and European beech in Bavaria, South Germany. In: Matzner E. (Ed). Biogeochemistry of Forested Catchments in a Changing Environment (2004), Springer, Berlin 271-278
6. Berg B., and McClaugherty C. Plant Litter, Decomposition, Humus Formation, Carbon Sequestration (2003), Springer-Verlag, Berlin, Heidelberg New York
7. Criquet S., Farnet A.M., Tagger S., and Le Petit J. Annual variations of phenoloxidase activities in an evergreen oak litter: influence of certain biotic and abiotic factors. Soil Biology & Biochemistry 32 (2000) 1505-1513
8. Dighton J. Nutrient cycling by saprotrophic fungi in terrestrial habitats. In: Wicklow D.T., and Söderström B. (Eds). The Mycota, Volume IV: Environmental and Microbial Relationships (1997), Springer, Berlin 271-279
9. Edwards I.P., Upchurch R.A., and Zak D.R. Isolation of fungal cellobiohydrolase I genes from sporocarps and forest soils by PCR. Applied and Environmental Microbiology 74 (2008) 3481-3489
10. Excoffier L., Laval G., and Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1 (2005) 47-50
11. FAO-UNESCO. Soil Map of the World, Revised Legend (1990), FAO, Rome World Soil Resources Report 60
12. Frankland J.C. Fungal succession - unraveling the unpredictable. Mycological Research 102 (1998) 1-15
13. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41 (1999) 95-98
14. - deposition in a Northern Hardwood Forest?. Microbial Ecology 57 (2009) 728-739
15. Hoegger P.J., Kilaru S., James T.Y., Thacker J.R., and Kües U. Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences. FEBS Journal 273 (2006) 2308-2326
16. Izzo A., Agbowo J., and Bruns T.D. Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest. New Phytologist 166 (2005) 619-630
17. Kaiser K., Eusterhues K., Rumpel C., Guggenberger G., and Kögel-Knabner I. Stabilization of organic matter by soil minerals - investigations of density and particle-size fractions from two acid forest soils. Journal of Plant Nutrition and Soil Science 165 (2002) 451-459
18. Kellner H., Luis P., and Buscot F. Diversity of laccase-like multicopper oxidase (LMCO) genes in Morchellaceae: identification of genes potentially involved in extracellular activities related to plant litter decay. FEMS Microbiology Ecology 61 (2007) 153-163
19. Kellner H., Jehmlich N., Benndorf D., Hoffmann R., Rühl M., Hoegger P.J., Majcherczyk A., Kües U., von Bergen M., and Buscot F. Detection, quantification and identification of fungal extracellular laccases using polyclonal antibody and mass spectrometry. Enzymes and Microbial Technology 41 (2007) 694-701
20. Kellner H., Luis P., Zimdars B., Kiesel B., and Buscot F. Diversity of bacterial laccase-like multicopper oxidase genes in forest and grassland Cambisol soil samples. Soil Biology & Biochemistry 40 (2008) 638-648
21. Kögel-Knabner I. The macromolecular composition of plant and microbial residues as inputs to soil organic matter. Soil Biology & Biochemistry 34 (2002) 139-162
22. Koide K., Osono T., and Takeda H. Fungal succession and decomposition of Camellia japonica leaf litter. Ecological Research 20 (2005) 599-609
23. Lauber C.L., Sinsabaugh R.L., and Zak D.R. Laccase gene composition and relative abundance in Oak forest soil is not affected by short-term nitrogen fertilization. Microbial Ecology 57 (2009) 50-57
24. Lozupone C. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71 (2005) 8228-8235
25. Luis P., Walther G., Kellner H., Martin F., and Buscot F. Diversity of laccase genes from basidiomycetes in a forest soil. Soil Biology & Biochemistry 36 (2004) 1025-1036
26. Luis P., Kellner H., Martin F., and Buscot F. A molecular method to evaluate basidiomycete laccase gene expression in forest soils. Geoderma 128 (2005) 18-27
27. Luis P., Kellner H., Zimdars B., Langer U., Martin F., and Buscot F. Patchiness and spatial distribution of laccase genes of ectomycorrhizal, saprotrophic and unknown basidiomycetes in the upper horizons of a mixed forest Cambisol. Microbial Ecology 50 (2005) 570-579
28. McCune B., and Mefford M.J. PC-Ord. Multivariate Analysis of Ecological Data, Version 4 (1999), MjM Software Design, Gleneden Beach, OR
29. O'Brien H.E., Parrent J.L., Jackson J.A., Moncalvo J.M., and Vilgalys R. Fungal community analysis by large-scale sequencing of environmental samples. Applied and Environmental Microbiology 71 (2005) 5544-5550
30. Osono T. Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Canadian Journal of Microbiology 52 (2006) 701-716
31. Osono T. Ecology of ligninolytic fungi associated with leaf litter decomposition. Ecological Research 22 (2007) 955-974
32. Osono T., and Takeda H. Organic chemical and nutrient dynamics in decomposing beech leaf litter in relation to fungal ingrowth and succession during 3-year decomposition processes in a cool temperate deciduous forest in Japan. Ecological Research 16 (2001) 649-670
33. Reynolds J., Weir B.S., and Cockerham C.C. Estimation for the coancestry coefficient: basis for a short-term genetic distance. Genetics 105 (1983) 767-779
34. Rosenbrock P., Buscot F., and Munch J.C. Fungal succession and changes in the fungal degradation potential during the initial stage of litter decomposition in a black forest (Alnus glutinosa (L.) Gaertn.). European Journal of Soil Science 31 (1995) 1-11
35. Shannon C.E. A mathematical theory of communication. Bell System Technical Journal 27 (1948) 379-423
36. Slatkin M. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139 (1995) 457-462
37. Smith M.E., Douhan G.W., and Rizzo D.M. Ectomycorrhizal community structure in a xeric Quercus woodland based on rDNA sequence analysis of sporocarps and pooled roots. New Phytologist 174 (2007) 847-863
38. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4 (1998), Sinauer Associates, Sunderland, MA
39. Tate R.L. Microbiology and enzymology of carbon and nitrogen cycling. In: Burns R.G., and Dick R.P. (Eds). Enzymes in the Environment (2002), Marcel Dekker, New York 267-284
40. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Smirnov S., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J., and Natale D.A. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4 (2003) 41
41. Tedersoo L., Kõljalg U., Hallenberg N., and Larsson K.H. Fine scale distribution of ectomycorrhizal fungi and roots across substrate layers including coarse woody debris in a mixed forest. New Phytologist 159 (2003) 153-165
42. Thon M.R., and Royse D.J. Partial beta-tubulin gene sequences for evolutionary studies in the Basidiomycotina. Mycologia 91 (1999) 468-474
43. Thorn G. The fungi in soil. In: van Elsaß J.D., Trevors J.T., and Wellington E.M.H. (Eds). Modern Soil Microbiology (1997), Marcel Dekker, New York 63-128
44. von Lützow M., Kögel-Knabner I., Ekschmitt K., Matzner E., Guggenberger G., Marschner B., and Flessa H. Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions - a review. European Journal of Soil Science 57 (2006) 426-445
45. Zak D.R., Blackwood C.B., and Waldrop M.P. A molecular dawn for biogeochemistry. Trends in Ecology & Evolution 21 (2006) 288-295