Assessing fungal diversity in soil, using the microarray chip technology
DFG RA 731/9-1
From 02/2006 to 12/2009Principal Investigator: Gerhard Rambold
Staff: Derek Peršoh
In a study published by Derek Peršoh, Alfons R. Weig, and Gerhard Rambold, the researchers introduced the EcoChip, a functional biodiversity microarray designed to analyze fungal communities in environmental samples with extensive functional and phylogenetic coverage. This innovative tool is able to integrate nucleic acid sequence data from large-scale sequencing projects as they become available. The EcoChip is unique in that it uses a dual probe set (DPS) developed to detect functional enzyme transcripts and phylogenetic barcoding transcripts. The probes targeting conserved protein domains detect functional genes, while the phylogenetic barcoding probes target ITS regions in precursor rRNA, marking the first time ITS precursor rRNA has been detected in a microarray experiment. The methodology of the EcoChip departs from traditional GeoChip-type microarrays, as it uses dedicated barcoding probes to obtain phylogenetic information while analyzing functional gene expression through domain-specific probes. This separation addresses the challenge of limited sequence information for functional enzyme-coding genes in environmental communities, offering a more comprehensive understanding of fungal activity. The EcoChip has been successfully applied to identify specific degradation activities in environmental samples with high phylogenetic resolution. The results showed that reproducible and unbiased microarray signals could be achieved using chemically labeled total RNA preparations, eliminating the need for enzymatic labeling steps. Together, these advancements demonstrate the EcoChip’s capability to selectively quantify the transcriptionally active components of fungal communities, making it a powerful tool for mycological studies in environmental science.
List of publications of this Project
| Weig, A R; Peršoh, D; Rambold, G: EcoChips für die Erforschung mikrobieller Lebensgemeinschaften, BIOspektrum, 19(4), 382–385 (2013), doi:10.1007/s12268-013-0326-9 -- Details |
| Peršoh, D; Weig, A; Rambold, G: A transcriptome-targeting EcoChip for assessing functional mycodiversity, Microarrays, 1, 25–41 (2012), doi:10.3390/microarrays1010025 -- Details |