Correlation of Methane Production and Functional Gene Transcriptional Activity in a Peat Soil

Abstract

The transcription dynamics of subunit A of the key gene in methanogenesis (methyl coenzyme M reductase; mcrA) was studied to evaluate the relationship between process rate (methanogenesis) and gene transcription dynamics in a peat soil ecosystem. Soil methanogen process rates were determined during incubation of peat slurries at temperatures from 4 to 37°C, and real-time quantitative PCR was applied to quantify the abundances of mcrA genes and transcripts; corresponding transcriptional dynamics were calculated from mcrA transcript/gene ratios. Internal standards suggested unbiased recovery of mRNA abundances in comparison to DNA levels. In comparison to those in pure-culture studies, mcrA transcript/gene ratios indicated underestimation by 1 order of magnitude, possibly due to high proportions of inactive or dead methanogens. Methane production rates were temperature dependent, with maxima at 25°C, but changes in abundance and transcription of the mcrA gene showed no correlation with temperature. However, mcrA transcript/gene ratios correlated weakly (regression coefficient ‫؍‬ 0.76) with rates of methanogenesis. Methanogen process rates increased over 3 orders of magnitude, while the corresponding maximum transcript/gene ratio increase was only 18-fold. mcrA transcript dynamics suggested steady-state expression in peat soil after incubation for 24 and 48 h, similar to that in stationary-phase cultures. mcrA transcript/gene ratios are therefore potential in situ indicators of methanogen process rate changes in complex soil systems.

Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil

“…These results could be related to differences in the rates of substrate production between treatments and indicated that energy substrates were the limited factors to microbial growth and activity. While both mcrA gene and transcript abundances were positively correlated with methane production, transcript abundance was more significant, as observed in other studies (Freitag and Prosser 2009;Ma et al 2012;Xu et al 2012), indicating that the variations of mcrA transcript abundance were more powerful in predicting CH 4 production. We analyzed the succession and dynamics of the methanogenic community with the purpose of understanding the effects of straw and nitrate addition.…”

Nitrogen and methanogen community composition within and among three Sphagnum dominated peatlands in Scandinavia

“…The medians of mcrA gene and transcripts copy numbers found in our three sites were relatively low as compared with previously reported numbers for an ombrotrophic upland blanket peat and a blanket peat bog also using qPCR for the mcrA quantification, but obtained by applying different primers (Freitag and Prosser, 2009;Freitag et al, 2010). Our study sites also showed relatively lower diversity of the mcrA gene compared to minerotrophic peatlands Juottonen et al, 2005;Merila et al, 2006).…”

Agricultural biogas production in Germany - from practice to microbiology basics

“…The activity of methanogens can be assessed by analysis of mcrA/mrtA transcripts, since it has been shown in several reports, e.g. [66,67], that mRNA transcribed from this gene (and measured as cDNA) correlates with methane production. Important differences between the composition of the total (DNA level) and the active (mRNA or cDNA level) population of methanogens were noticed, e.g.…”

“…All of these factors have a huge impact on the result, and different methods applied in different laboratories can be the source of considerable variation of results [89]. It is therefore essential to optimize sampling, sample processing and analysis, and to assess and report DNA and RNA recovery rates [66,67] by quantifying the losses of the complete system, i.e., between the first sample preparation and the last analytical detection step, e.g., in a sample spiking approach. Results obtained with different methods cannot be compared if this information is not provided.…”