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Wetlands are important sources of the greenhouse gas methane (CH4). We provide an in situ study of CH4 dynamics in the permanently submerged soil of a Swiss alpine fen. Physico-chemical pore water analyses were combined with structural and microbiological analyses of soil cores at high vertical resolution down to 50 cm depth. Methanotrophs and methanogens were active throughout the depth profile, and highest abundance of active methanotrophs and methanogens [6.1 × 10(5) and 1.1 × 10(7) pmoA and mcrA transcripts (g soil)(-1), respectively] was detected in the uppermost 2 cm of the soil. Active methanotrophic communities in the near-surface zone, dominated by viable mosses, varied from the communities in the deeper zones, but further changes with depth were not pronounced. Apart from a distinct active methanogenic community in the uppermost sample, a decrease of acetoclastic Methanosaetaceae with depth was observed in concomitance with decreasing root surface area. Overall, root surface area correlated with mcrA transcript abundance and CH4 pore water concentrations, which peaked (137.1 μM) at 10 to 15 cm depth. Our results suggest that stimulation of methanogenesis by root exudates of vascular plants had a stronger influence on CH4 dynamics than stimulation of CH4 oxidation by O2 input., (© FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Aerobic methane-oxidizing bacteria (MOB) play an important role in soils, mitigating emissions of the greenhouse gas methane (CH(4)) to the atmosphere. Here, we combined stable isotope probing on MOB-specific phospholipid fatty acids (PLFA-SIP) with field-based gas push-pull tests (GPPTs). This novel approach (SIP-GPPT) was tested in a landfill-cover soil at four locations with different MOB activity. Potential oxidation rates derived from regular- and SIP-GPPTs agreed well and ranged from 0.2 to 52.8 mmol CH(4) (L soil air)(-1) day(-1). PLFA profiles of soil extracts mainly contained C(14) to C(18) fatty acids (FAs), with a dominance of C(16) FAs. Uptake of (13) C into MOB biomass during SIP-GPPTs was clearly indicated by increased δ(13)C values (up to c. 1500‰) of MOB-characteristic FAs. In addition, (13)C incorporation increased with CH(4) oxidation rates. In general, FAs C(14:0) , C(16:1ω8), C(16:1ω7) and C(16:1ω6) (type I MOB) showed highest (13)C incorporation, while substantial (13)C incorporation into FAs C(18:1ω8) and C(18:1ω7) (type II MOB) was only observed at high-activity locations. Our findings demonstrate the applicability of the SIP-GPPT approach for in situ quantification of potential CH(4) oxidation rates and simultaneous labelling of active MOB, suggesting a dominance of type I MOB over type II MOB in the CH(4)-oxidizing community in this landfill-cover soil., (© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Recently, a unique microbial community, growing in a whitish, macroscopically visible strings-of-pearls-like structure was discovered in the cold, sulfidic marsh water of the Sippenauer Moor near Regensburg, Bavaria, Germany. The pearls interior is predominated by microcolonies of the non-methanogenic SM1 euryarchaeon; the outer part of the pearls is mainly composed of Thiothrix. To screen sulfidic ecosystems for the distribution of such unique microbial communities, comparative microbial and geochemical analyses of cold, sulfidic springs of three geographically distinct locations in Bavaria, Germany, and Dalyan, Turkey, were performed. Here, we report on the discovery and study of another type of strings-of-pearls revealing a new microbial community structure. While the SM1 euryarchaeon is again the predominant archaeal constituent, the bacterial partner is the so-called IMB1 eta-proteobacterium. Due to the predominance of the IMB1 eta-proteobacterium, the strings-of-pearls reveal a fluffy and greyish macroscopical appearance. The phylogenetic survey revealed SM1 euryarchaeal relatives, designated as SM1 group, in all sites studied, indicating a widespread distribution of these archaea in terrestrial ecosystems.