Methanotrophic and Methanogenic Communities in Swiss Alpine Fens Dominated by Carex rostrata and Eriophorum angustifolium

Abstract

Vascular plants play a key role in controlling CH 4 emissions from natural wetlands, because they influence CH 4 production, oxidation, and transport to the atmosphere. Here we investigated differences in the abundance and composition of methanotrophic and methanogenic communities in three Swiss alpine fens dominated by different vascular plant species under natural conditions. The sampling locations either were situated at geographically distinct sites with different physicochemical properties but the same dominant plant species (Carex rostrata) or were located within the same site, showing comparable physicochemical pore water properties, but had different plant species (C. rostrata or Eriophorum angustifolium). All three locations were permanently submerged and showed high levels of CH 4 emissions (80.3 to 184.4 mg CH 4 m ؊2 day ؊1 ). Soil samples were collected from three different depths with different pore water CH 4 and O 2 concentrations and were analyzed for pmoA and mcrA gene and transcript abundance and community composition, as well as soil structure. The dominant plant species appeared to have a significant influence on the composition of the active methanotrophic communities (transcript level), while the methanogenic communities differed significantly only at the gene level. Yet no plant species-specific microbial taxa were discerned. Moreover, for all communities, differences in composition were more pronounced with the site (i.e., with different physicochemical properties) than with the plant species. Moreover, depth significantly influenced the composition of the active methanotrophic communities. Differences in abundance were generally low, and active methanotrophs and methanogens coexisted at all three locations and depths independently of CH 4 and O 2 concentrations or plant species.T he atmospheric concentration of the highly potent greenhouse gas methane (CH 4 ) has increased over the past several decades to a current value of ca. 1.8 ppm by volume (ppmv) and is continuing to rise after an apparent stagnation in the early 2000s (1). Natural wetlands are the most important nonanthropogenic CH 4 source, with estimated emissions of 177 to 284 Tg year Ϫ1 , accounting for 26 to 42% of the global CH 4 budget (2). Wetlands in northern high latitudes (north of 45°N) contribute approximately 44.0 to 53.7 Tg CH 4 year Ϫ1 (3). The CH 4 cycle in these environments is driven by microorganisms: methanogenic archaea (methanogens) generate CH 4 in the anoxic zones of the wetland soil as the terminal step of anaerobic degradation of organic matter. These microorganisms represent a monophyletic euryarchaeal lineage and largely utilize hydrogen or carbon dioxide, acetate, or small methylated compounds as substrates (4, 5). On the other hand, a substantial amount of CH 4 generated in wetlands is oxidized before it can reach the atmosphere by aerobic methaneoxidizing bacteria (methanotrophs), which are active mainly at the oxic-anoxic interface (6). These organisms can utilize CH 4 as the sole energy and carbon...

Occurrence and Origin of Methane Entrapped in Sediments and Rocks of a Calcareous, Alpine Glacial Catchment

“…Total RNA was extracted from ~2.5 g of the waterlogged samples using the RNA PowerSoil® Total RNA Isolation Kit (MO BIO Laboratories) according to the manufacturer's instructions. Removal of residual DNA, purification, and reverse transcription were performed as described previously (Cheema et al, ). Complete removal of DNA originating from methanogens after DNase digestion was tested by subjecting the RNA to PCR with mcrA ‐specific primers (see below and Table S3).…”

“…Abundance of genes (DNA) and transcripts (cDNA) of mcrA per gram soil (wet weight) was determined by quantitative PCR as described by Cheema et al (). A total of two runs was required to include all the samples.…”

A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments

“…It belonged to the phylogenetic cluster containing PmoA sequences from gammaproteobacterial methanotrophs and formed a novel, genus-level lineage, which was only distantly related (81-86% amino acid identity) to the PmoA cluster defined by the genera Methylococcus, Methylocaldum and Methylogaea (Figure 2a). Notably, this PmoA lineage included a number of sequences obtained in cultivation-independent studies from various freshwater environments, that is, peatlands, lake sediments, boreal forest and alpine fen soils (Pester et al, 2004;Jaatinen et al, 2005;Bussmann et al, 2006;Danilova and Dedysh, 2014;Cheema et al, 2015;Danilova et al, 2015). This PmoA lineage is also addressed as OSC (Organic Soil Cluster) cluster of uncultivated methanotrophs, which occur predominantly in peatlands and in some upland soils (Knief, 2015).…”

Impacts of temperature and soil characteristics on methane production and oxidation in Arctic polygonal tundra

“…Given that half-saturation constants for CH 4 and O 2 used in methanotrophy models vary over 1-2 orders of 15 magnitude (Segers, 1998;Riley et al, 2011), aerobic CH 4 oxidation could occur throughout much of the soil column, as advective, diffusive or plant-mediated transport processes introduce O 2 into the soil. Others have observed deep soil CH 4 oxidation activity in peatlands (Hornibrook et al, 2009), fens (Cheema et al, 2015) and wet tundra (Barbier et al, 2012), often correlated with water table depth (Sundh et al, 1994).…”