Methyl coenzyme M reductase (mcrA) gene abundance correlates with activity measurements of methanogenic H₂/CO₂‐enriched anaerobic biomass

Abstract

Biologically produced methane (CH4) from anaerobic digesters is a renewable alternative to fossil fuels, but digester failure can be a serious problem. Monitoring the microbial community within the digester could provide valuable information about process stability because this technology is dependent upon the metabolic processes of microorganisms. A healthy methanogenic community is critical for digester function and CH4 production. Methanogens can be surveyed and monitored using genes and transcripts of mcrA, which encodes the α subunit of methyl coenzyme M reductase – the enzyme that catalyses the final step in methanogenesis. Using clone libraries and quantitative polymerase chain reaction, we compared the diversity and abundance of mcrA genes and transcripts in four different methanogenic hydrogen/CO2 enrichment cultures to function, as measured by specific methanogenic activity (SMA) assays using H2/CO2. The mcrA gene copy number significantly correlated with CH4 production rates using H2/CO2, while correlations between mcrA transcript number and SMA were not significant. The DNA and cDNA clone libraries from all enrichments were distinctive but community diversity also did not correlate with SMA. Although hydrogenotrophic methanogens dominated these enrichments, the results indicate that this methodology should be applicable to monitoring other methanogenic communities in anaerobic digesters. Ultimately, this could lead to the engineering of digester microbial communities to produce more CH4 for use as renewable fuel.

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

“…Our results indicating reduced decomposition potential under deeper snowpack are consistent with other long-term warming and snow fence studies from Arctic tundra ecosystems that report zero net C loss (or even C gain) during the growing season (Natali et al, 2012Sistla et al, 2013). We speculate that initial soil conditions likely favour decomposer activity and decomposition rates increase in response to increased temperatures, resulting in C loss.…”

“…The initial effects of increased snowpack result in altered physical factors (greater active layer thaw depth and increased soil temperatures and moisture; Blanc-Betes et al, 2016) which may lead to increased SOM availability and faster enzyme activities with the potential to enhance SOM decomposition. Higher SOM mineralization may promote the documented shifts in aboveground plant communities and increased NPP (Natali et al, 2012;Sturm et al, 2005;Anderson-Smith, 2013), and vege-tation shifts to more shrubby species may alter the chemistry and quality of new litter inputs, ultimately affecting decomposer communities. Moreover, soil moisture and compaction can reduce O 2 diffusion into the soil, inhibiting aerobic SOM decomposition (Blanc-Betes et al, 2016;O'Brien et al, 2010), and altering bacterial community composition by selecting for microorganisms that utilize simple C substrates, leaving behind complex organic compounds and plant polymers.…”

“…Furthermore, gene abundance in itself is not a direct measurement of gene expression or enzyme activity (Wood et al, 2015). However, it does provide a measure of genetic potential and may be positively correlated with enzyme activity and gene expression (Morris et al, 2014;Neufeld et al, 2001;Rocca et al, 2014). Accurate measurement of enzymatic functional potential or gene expression would require a targeted metagenomic and metatranscriptomic approach.…”

“…Also, microbial mineralization of plant nutrients, such as nitrogen (N) and phosphorus (P), from SOM decomposition are likely to contribute to increased net primary productivity (NPP; Hinzman et al, 2005;Natali et al, 2012;Pattison and Welker, 2014) and cause shifts in vegetation from herbaceous species (cottongrass tussock -Eriophorum vaginatum) towards woody species (Arctic shrubs -Betula nana and Salix pulchra) that may produce a larger amount of plant litter compounds that are more resistant to decomposition (Bret-Harte et al, 2001;Pearson et al, 2013;Sturm et al, 2005;Wahren, 2005). The balance between these processes will determine the extent to which Arctic tundra ecosystems feedback on the global climate, making the fate of this stored C unclear (Sistla et al, 2013).…”

Quantitative detection of syntrophic fatty acid-degrading bacterial communities in methanogenic environments

“…From a practical standpoint, this technique has been successfully used in combination with analytical methods to relate methanogen abundance and dynamics to digester function (Hori et al, 2006;Yu et al, 2006;Morris et al, 2014). In this study, we report the development of four genus-specific qPCR assays, based on the 16S rRNA gene, for the quantification of known SFAB within the genera Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas.…”