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ARS Home » Pacific West Area » Pullman, Washington » Northwest Sustainable Agroecosystems Research » Research » Publications at this Location » Publication #254390
Title: Detection of mRNAs in soils using targeted microarrays for genes associated with lignin degradation

Author
item BAILEY, VANESSA - Pacific Northwest National Laboratory
item FANSLER, SARAH - Pacific Northwest National Laboratory
item BANDYOPADHYAY, SOMNATH - Novartis Institutes
item Smith, Jeffrey
item WATERS, KATRINA - Pacific Northwest National Laboratory
item BOLTON, HARVEY - Pacific Northwest National Laboratory

Submitted to: Soil Biology and Biochemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2010
Publication Date: 7/4/2010
Citation: Bailey, V.L., Fansler, S.J., Bandyopadhyay, S., Smith, J.L., Waters, K.M., Bolton, H. 2010. Detection of mRNAs in soils using targeted microarrays for genes associated with lignin degradation. Soil Biology and Biochemistry. 42(10):1793-1799.

Interpretive Summary: Comparisons of soils on a microbial basis are difficult due to the wide diversity of microbial communities and the lack of specific methods. Using a different technique we were able to detect fungally derived lignin-degrading enzymes in soils. We found that restored prairie soil exhibited greater induced lignin degrading enzymes than a farmed agricultural soil. This is an important finding that suggests prairie soils without tillage may offset their carbon storage capacity by degrading recalcitrant lignin faster than agricultural soils. This information will have an impact for scientists studying soil carbon storage and environmental modelers developing carbon cycling models.

Technical Abstract: Microarrays have become established tools for describing microbial systems, however the direct assessment of expression profiles for uncharacterized environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus we apply a target labeling and amplification approach based on the Klenow fragment and signal amplification approach to detect expression of fungally derived lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of genes potentially encoding lignin-degrading enzymes following incubation with lignin substrate, while a farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA does interfere with detection of the low abundance transcripts, nevertheless this microarray approach consistently reports the higher-abundance transcripts which present more robust signals.