Dataset Information

GNPS - 20230206 - Lignin ligands-quinones-permafrost soil extracts

ABSTRACT: It includes analysis of different types of organic carbon 1 Model ligands and complexes 2 Lignin degradation materials 3 Quinones and adducts from biochars 4 Extraction and porewater of permafrost soils across the gradients of palsa-bog-fens

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Environmental Samples <bacillariophyta> (ncbitaxon:33858)

SUBMITTER: Daniel Petras

PROVIDER: MSV000091211 | GNPS | Mon Feb 06 08:43:00 GMT 2023

REPOSITORIES: GNPS

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for 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 signal amplification approach, rather than template amplification, to analyze the expression of selected 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 lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals. Keywords: comparative analysis, microbial ecology, soil microbial communities We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.

Dataset Information

GNPS - 20230206 - Lignin ligands-quinones-permafrost soil extracts

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets