Quantitative PCR for measuring biomass of decomposer fungi in planta

Fungal Ecology

Volumn 7, Issue 1, 2014, Pages 39-46

  Song, Zewei ^a   Vail, Andrew ^a   Sadowsky, M J ^a   Schilling, Jonathan S ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Biomass; Ergosterol; Fungi; Quantitative PCR; Wood decomposition

Indexed keywords

EID: 84893097180     PISSN: 17545048     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funeco.2013.12.004     Document Type: Article

References (39)

1. Bååth E. Estimation of fungal growth rates in soil using 14 C-acetate incorporation into ergosterol. Soil Biology and Biochemistry 2001, 33:2011-2018.
2. Baldrian P., Větrovský T., Cajthaml T., Dobiášová P., Petránková M., Šnajdr J., Eichlerová I. Estimation of fungal biomass in forest litter and soil. Fungal Ecology 2013, 6:1-11.
3. Boddy L. Interspecific combative interactions between wood-decaying basidiomycetes. FEMS Microbiology Ecology 2000, 31:185-194.
4. Coetzee M., Wingfield B., Harrington T. Geographical diversity of Armillaria mellea s. s. based on phylogenetic analysis. Mycologia 2000, 92:105-113.
5. de Graaff M.A., Classen A.T., Castro H.F., Schadt C.W. Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates. The New Phytologist 2010, 188:1055-1064.
6. Eikenes M., Hietala A.M., Alfredsen G., Fossdal C.G., Solheim H. Comparison of quantitative real-time PCR,chitin and ergosterol assays for monitoring colonization of Trametes versicolor in birch wood. Holzforschung 2005, 59:568-573.
7. Ekblad A., Wallander H., Näsholm T. Chitin and ergosterol combined to measure total and living fungal biomass in ectomycorrhizas. The New Phytologist 1998, 138:143-149.
8. Fierer N., Jackson J., Vilgalys R., Jackson R. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology 2005, 71:4117-4120.
9. Franklin J.F., Shugart H.H., Harmon M.E. Tree death as an ecological process. Bioscience 1987, 37:550-556.
10. Fraver S., Milo A.M., Bradford J.B., D'Amato A.W., Kenefic L., Palik B.J., Woodall C.W., Brissette J. Woody debris volume depletion through decay: implications for biomass and carbon accounting. Ecosystems 2013, 16:1262-1272.
11. Freschet G.T., Weedon J.T., Aerts R., van Hal J.R., Cornelissen J.H.C. Interspecific differences in wood decay rates: insights from a new short-term method to study long-term wood decomposition. Journal of Ecology 2012, 100:161-170.
12. Fukami T., Dickie I.A., Paula Wilkie J., Paulus B.C., Park D., Roberts A., Buchanan P.K., Allen R.B. Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecology Letters 2010, 13:675-684.
13. Hale C.M., Pastor J. Nitrogen content, decay rates, and decompositional dynamics of hollow versus solid hardwood logs in hardwood forests of Minnesota, U.S.A. Canadian Journal of Forest Research 1998, 28:1276-1285.
14. Harris S. Branching of fungal hyphae: regulation, mechanisms and comparison with other branching systems. Mycologia 2008, 100:823-832.
15. Herrera M.L., Vallor A.C., Gelfond J.A., Patterson T.F., Wickes B.L. Strain-dependent variation in 18S ribosomal DNA Copy numbers in Aspergillus fumigatus. Journal of Clinical Microbiology 2009, 47:1325-1332.
16. Horisawa S., Sakuma Y., Doi S. Qualitative and quantitative PCR methods using species-specific primer for detection and identification of wood rot fungi. Journal of Wood Science 2009, 55:133-138.
17. Jasalavich C.A., Ostrofsky A., Jellison J. Detection and identification of decay fungi in spruce wood by restriction fragment length polymorphism analysis of amplified genes encoding rRNA. Applied and Environmental Microbiology 2000, 66:4725-4734.
18. Jones H., Worrall J. Fungal biomass in decayed wood. Mycologia 1995, 87:459-466.
19. Kennedy P.G., Hortal S., Bergemann S.E., Bruns T.D. Competitive interactions among three ectomycorrhizal fungi and their relation to host plant performance. Journal of Ecology 2007, 95:1338-1345.
20. Klamer M., Bååth E. Estimation of conversion factors for fungal biomass determination in compost using ergosterol and PLFA 18:2ω6,9. Soil Biology and Biochemistry 2004, 36:57-65.
21. Klein D.A., Paschke M.W. Filamentous fungi: the indeterminate lifestyle and microbial ecology. Microbial Ecology 2004, 47:224-235.
22. Kramer K., Muthukrishnan S. Insect chitinases: molecular biology and potential use as biopesticides. Insect Biochemistry and Molecular Biology 1998, 27:887-900.
23. Kubartová A., Ottosson E., Dahlberg A., Stenlid J. Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing. Molecular Ecology 2012, 21:4514-4532.
24. Li Y., Wadsö L., Larsson L. Impact of temperature on growth and metabolic efficiency of Penicillium roqueforti - correlations between produced heat, ergosterol contentand biomass. Journal of Applied Microbiology 2009, 106:1494-1501.
25. López-Mondéjar R., Antón A., Raidl S., Ros M., Pascual J.A. Quantification of the biocontrol agent Trichoderma harzianum with real-time TaqMan PCR and its potential extrapolation to the hyphal biomass. Bioresource Technology 2010, 101:2888-2891.
26. Maleszka R. Electrophoretic analysis of the nuclear and organellar genomes in the ultra-small alga Cyanidioschyzon merolae. Current Genetics 1993, 24:548-550.
27. Meier C.L., Rapp J., Bowers R.M., Silman M., Fierer N. Fungal growth on a common wood substrate across a tropical elevation gradient: temperature sensitivity, community composition, and potential for above-ground decomposition. Soil Biology and Biochemistry 2010, 42:1083-1090.
28. Newell S.Y., Miller J.D., Fallon R.D. Ergosterol content of salt-marsh fungi: effect of growth conditions and mycelial age. Mycologia 1987, 79:688-695.
29. Newell S., Arsuffi T., Fallon R. Fundamental procedures for determining ergosterol content of decaying plant material by liquid chromatography. Applied and Environmental Microbiology 1988, 54:1876-1879.
30. Park J.W., Crowley D.E. Normalization of soil DNA extraction for accurate quantification of target genes by real-time PCR and DGGE. BioTechniques 2005, 38:579-586.
31. Pasanen A.L., Yli-Pietilä K., Pasanen P., Pentti Kalliokoski A., Tarhanen J. Ergosterol content in various fungal species and biocontaminated building materials. Applied and Environmental Microbiology 1999, 65:138-142.
32. Raidl S., Bonfigli R., Agerer R. Calibration of quantitative real-time TaqMan PCR by correlation with hyphal biomass and ITS copies in mycelia of Piloderma croceum. Plant Biology 2005, 7:713-717.
33. Raviraja N.S., Nikolcheva L.G., Bärlocher F. Pellet size affects mycelial ergosterol content in aquatic hyphomycetes. Mycologia 2004, 96:388-392.
34. Ruzicka S., Edgerton D., Norman M., Hill T. The utility of ergosterol as a bioindicator of fungi in temperate soils. Soil Biology and Biochemistry 2000, 32:989-1005.
35. Scheu S., Parkinson D. Changes in bacterial and fungal biomass C, bacterial and fungal biovolume and ergosterol content after drying, remoistening and incubation of different layers of cool temperate forest soils. Soil Biology and Biochemistry 1994, 26:1515-1525.
36. Schilling J.S., Jellison J. Oxalate regulation by two brown rot fungi decaying oxalate-amended and non-amended wood. Holzforschung 2005, 59:681-688.
37. Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W. Nuclear ribosomal internal transcribed spacer ITS region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 2012, 109:6241-6246.
38. Singh T., Vesentini D., Singh A.P., Daniel G. Effect of chitosan on physiological, morphological, and ultrastructural characteristics of wood-degrading fungi. International Biodeterioration & Biodegradation 2008, 62:116-124.
39. Song Z., Vail A., Sadowsky M.J., Schilling J.S. Competition between two wood-degrading fungi with distinct influences on residues. FEMS Microbiology Ecology 2012, 79:109-117.