Reverse transcription-PCR methods significantly impact richness and composition measures of expressed fungal cellobiohydrolase I genes in soil and litter

Journal of Microbiological Methods

Volumn 86, Issue 3, 2011, Pages 344-350

  Weber, Carolyn F ^a   Kuske, Cheryl R ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Cellobiohydrolase I; Fungi; Gene expression; RT PCR; SMART PCR; Soil

Indexed keywords

CELLULOSE 1,4 BETA CELLOBIOSIDASE; COMPLEMENTARY DNA; DOUBLE STRANDED DNA; FUNGAL RNA; GLYCOSIDASE; SINGLE STRANDED DNA;

ARTICLE; CELLOBIOHYDROLASE 1 GENE; CONTROLLED STUDY; DNA LIBRARY; FOREST SOIL; FUNGAL GENE; GENE AMPLIFICATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; MULTIGENE FAMILY; NONHUMAN; PLANT LITTER; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SPECIES COMPOSITION; SPECIES RICHNESS;

CELLULOSE 1,4-BETA-CELLOBIOSIDASE; DNA PRIMERS; DNA, FUNGAL; FUNGI; GARBAGE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE LIBRARY; GENES, FUNGAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

EUKARYOTA; FUNGI;

EID: 79960637979     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2011.06.011     Document Type: Article

References (37)

1. Andersen I., Cariney J.W.G. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environmental Microbiology 2004, 6:769-779.
2. Andersen I., Parkin P.I. Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules. Journal of Micorbiological Methods 2007, 68:248-253.
3. Arnaud M.B., Chibucos M.C., Costanzo M.C., Crabtree J., Inglis D.O., Lotia A., et al. The Aspergillus genome database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Research 2010, 38:D420-D427.
4. Bailly J., Fraissinet-Tachet L., Verner M.-C., Debaud J.-C., Lemaire M., Wesolowski-Louvel M., Marmeisse R. Soil eukaryotic functional diversity, a metatranscriptomic approach. The ISME Journal. 2007, 1:632-642.
5. Birney E., Clamp M., Durbin R. GeneWise and Genomewise. Genome Research 2004, 14:988-995.
6. Bjorbækmo M.F.M., Carlsen T., Brysting A., Vralstad T., Holand K., Ugland K.I., et al. High diversity of root associated fungi in both alpine and arctic Dryas octopetala. BMC Plant Biology 2010, 10:244.
7. Borneman J., Triplett E.W. Rapid and direct method for extraction of RNA from soil. Soil Biology and Biochemistry. 1997, 29:1621-1624.
8. Breuninger M., Requena N. Recognition events in AM symbiosis: analysis of fungal gene expression at the early appressorium stage. Fungal Genetics and Biology 2004, 41:794-804.
9. Bridge P., Spooner B. Soil fungi: diversity and detection. Plant and Soil 2001, 232:147-154.
10. Clontech Laboratories Inc. SMARTer™ PCR cDNA Synthesis Kit User Manual. Version October 2009.
11. Courty P.E., Poletto M., Duchaussoy F., Buee M., Garbaye J., Martin F. Gene transcription in Lactarius quietus-Quercus petraea Ectomycorrhizas from a forest soil. Applied and Environmental Microbiology 2008, 74:6598-6605.
12. Edwards I., Upchurch R., Zak D. Isolation of fungal cellobiohydrolase I genes from sporocarps and forest soils by PCR. Applied and Environmental Micobiology 2008, 74:3481-3489.
13. Gregoriev, I.V., Cullen, D., Hibbett, D., Goodwin, S.B., Jeffries, T.W., Kubicek, C.P., Kuske, C., Magnuson, J., Martin, F., Spatafora, J., Tsang, A. and Baker, S. (in press) Fueling the future with fungal genomics. Mycology: An International Journal of Fungal Biology.
14. Hillmann A.G., Harmon S., Park S.D.E., O'Brien J., Shields D.C., Kenny D. Comparative rNA expression analyses from small-scale, single-donor platelet samples. Journal Thrombosis Haemostasis 2006, 4:349-356.
15. Hillmann A., Dunne E., Kenny D. cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR. DNA and RNA Profiling in Human Blood: Methods and Protocols 2009, vol. 496. Humana Press.
16. Kellner H., Zak D.R. Detection of expressed fungal type I polyketide synthase genes in forest soil. Soil Biology and Biochemistry 2009, 41:1344-1347.
17. Kellner H., Luis P., Schlitt B., Buscot F. Temporal changes in diversity and expression patterns of fungal laccase genes within the organic horizon of a brown forest soil. Soil Biology and Biochemistry 2009, 41:1380-1389.
18. Kellner H., Zak D.R., Vandenbol M. Fungi unearthed: transcripts encoding lignocellulolytic and chitinolytic enzymes in forest soil. PLoS One 2010, 5:1-6.
19. Kohler A., Delaruelle C., Martin D., Encelot N., Martin F. The poplar root transcriptome: analysis of 7000 expressed sequence tags. FEBS Letters 2003, 542:37-41.
20. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
21. Liew E.C.Y., Guo L.-D., Ranghoo V.M., Goh T.-K., Hyde K.D. Molecular approaches to assessing fungal diversity in the natural envrionment. Fungal Diversity 1998, 1:1-17.
22. Lu J., Liu T., Yu X., Lin F. Representative appressorium stage cDNA library of Magnaportha grisea. JZUS 2005, 6B:132-136.
23. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar A., et al. ARB: a software environment for sequence data. Nucleic Acids Research 2004, 32:1363-1371.
24. Luis P., Kellner H., Martin F., Buscot F. A molecular method to evaluate basidiomycete laccase gene expression in forest soils. Geoderma 2005, 128:18-27.
25. Martin F., Cullen D., Hibbett D., Pisabarro A., Spatafora J.W., Baker S.E., Gregoriev I.V. Sequencing the fungal tree of life. New Phytologist 2011, 1-4.
26. Martin-Laurent F., Philippot L., Hallet S., Chaussod J., Germon J.C., Soulas G., Catroux G. DNA extraction from soils: old bias for new microbial diversity analysis methods. Applied and Environmental Microbiology 2001, 67:2354-2359.
27. MoBio Laboratories, Inc. PowerSoil DNA Isolation Kit Instruction Manual. Version: 10222009.
28. Podila G.K., Zheng J., Balasubramanian, Sundaram S., Hiremath S., Brand J.H., Hymes M.J. Fungal gene expression in early symbiotic interactions between Laccaria bicolor and red pine. Plant and Soil 2002, 244:117-128.
29. Prentis P.J., Woolfit M., Thomas-Hall S.R., Ortiz-Barrientos D., Pavasovic A., Lowe A.J., Schenk P.M. Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Annals of Botany 2010, 106:1009-1017.
30. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7437-7541.
31. Sessitch A., Gyamfi S., Stralis-Pavese N. RNA isolation from soil for bacterial community and functional analysis: evaluation of different extraction and soil conservation protocols. Journal of Microbiological Methods 2002, 51:171-179.
32. Sole M., Kellner H., Brock S., Buscot F., Schlosser D. Extracellular laccase activity and transcript levels of putative laccase genes during removal of the xenoestrogen technical nonylphenol by the aquatic hyphomycete Clavariopsis aquatica. FEMS Microbiology Ecology 2009, 288:47-54.
33. Timmermans M.J.T.N., de Boer M.E., Nota B., de Boer T.E., Marien J., Klein-Lankhorst R., et al. Collembase: a repository for springtail genomics and soil quality assessment. BMC Genomics 2007, 8:341.
34. Weber, C.F., Zak, D.R., Hungate, B.A., Jackson, R.B., Vilgalys, R., Evans, R.D., Schadt, C.W., Megonigal, J.P. and Kuske, C.R. Responses of soil cellulolytic fungal communities to elevated atmospheric CO2 are complex and variable across five ecosystems. Environmental Microbiology (in press).
35. Webster J., Weber R.W.S. Introduction to Fungi 2007, Cambridge University Press, New York.
36. Wintzingerode F.V., Goebel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 1997, 21:213-229.
37. Zhumbayeva B., Diatchenko L., Chenchik A., Siebert P.D. Use of SMART-generated cDNA for gene expression studies in multiple human tumors. Biotechniques 2001, 30:158-163.