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Microarrays 2012, 1(1), 25-41; doi:10.3390/microarrays1010025
Article

A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity

1
, 2,*  and 1,2
Received: 1 September 2011; in revised form: 14 October 2011 / Accepted: 17 October 2011 / Published: 31 October 2011
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Abstract: A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory.
Keywords: active fungal community; soil; quantitative microarray; precursor rRNA; mRNA active fungal community; soil; quantitative microarray; precursor rRNA; mRNA
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Peršoh, D.; Weig, A.R.; Rambold, G. A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity. Microarrays 2012, 1, 25-41.

AMA Style

Peršoh D, Weig AR, Rambold G. A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity. Microarrays. 2012; 1(1):25-41.

Chicago/Turabian Style

Peršoh, Derek; Weig, Alfons R.; Rambold, Gerhard. 2012. "A Transcriptome—Targeting EcoChip for Assessing Functional Mycodiversity." Microarrays 1, no. 1: 25-41.

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