Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds.

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.

Abstract. We present the first high-resolution (500 m × 500 m) gridded methane (CH 4 ) emission inventory for Switzerland, which integrates 90 % of the national emission totals reported to the United Nations Framework Convention on Climate Change (UNFCCC) and recent CH 4 flux studies conducted by research groups across Switzerland. In addition to anthropogenic emissions, we also include natural and semi-natural CH 4 fluxes, i.e., emissions from lakes and reservoirs, wetlands, wild animals as well as uptake by forest soils. National CH 4 emissions were disaggregated using detailed geostatistical information on source locations and their spatial extent and process-or area-specific emission factors. In Switzerland, the highest CH 4 emissions in 2011 originated from the agricultural sector (150 Gg CH 4 yr −1 ), mainly produced by ruminants and manure management, followed by emissions from waste management (15 Gg CH 4 yr −1 ) mainly from landfills and the energy sector (12 Gg CH 4 yr −1 ), which was dominated by emissions from natural gas distribution. Compared with the anthropogenic sources, emissions from natural and semi-natural sources were relatively small (6 Gg CH 4 yr −1 ), making up only 3 % of the total emissions in Switzerland. CH 4 fluxes from agricultural soils were estimated to be not significantly different from zero (between −1.5 and 0 Gg CH 4 yr −1 ), while forest soils are a CH 4 sink (approx. −2.8 Gg CH 4 yr −1 ), partially offsetting other natural emissions. Estimates of uncertainties are provided for the different sources, including an estimate of spatial disaggregation errors deduced from a comparison with a global (EDGAR v4.2) and an European (TNO/MACC) CH 4 inventory. This new spatially explicit emission inventory for Switzerland will provide valuable input for regional-scale atmospheric modeling and inverse source estimation.

In the surface waters of sulfidic springs near Regensburg, Bavaria, Germany, the SM1 euryarchaeon, together with filamentous bacteria, forms the recently described unique string-of-pearls community. In addition to naturally occurring string-of-pearls communities, the growth of these communities was also observed on polyethylene nets provided as an artificial attachment material in the streamlets of springs. In order to learn more about the distribution and origin of the SM1 euryarchaeon and its possible occurrence in the subsurface, polyethylene nets were incubated as deeply as possible in different spring holes. After a short residence time, slime-like, milky drops, almost completely composed of SM1 euryarchaeon, were attached to the nets, indicating that this organism grows independent of a partner in deeper earth layers. A newly designed in situ biofilm trapping system allowed the quantitative harvesting of organisms exhibiting this newly discovered lifestyle of the SM1 euryarchaeon for detailed biological studies. The discovery of naturally occurring archaeal biofilms extends our knowledge of the biology and ecological significance of archaea in their environments.Sulfidic springs are fairly common around the world and have been the focus of (micro)biological work for more than 150 years (29, 42). They were classified as areas of high bioactivity, as visible by the development of extended (white) mats representing vast populations of various genera of filamentous sulfur bacteria (23). As the main focus for our detailed investigations of microbial communities in nongeothermal environments, we have chosen a sulfurous marsh, the "Sippenauer Moor" near Regensburg, Germany (32). In this area, cold water (ϳ10°C) from deeper earth layers reaches the surface and emerges from the ground between rocks and tree roots, forming small streamlets that merge in a large pond. The intake of atmospheric oxygen causes the appearance of white microbial mats in the streamlets, indicating high bioactivity. In these sulfidic streamlets, growth of a unique microbial community occurs, with microbes forming a string-of-pearls-like, macroscopically visible structure: single, whitish pearls with diameters of up to 3 mm are connected to each other by thin, white-colored threads. In the pearl interior, the nonmethanogenic SM1 euryarchaeon is predominant, representing a deep phylogenetic branch within the 16S rRNA tree (32). The exteriors of the pearls and the connecting threads are mainly composed of a single phylotype, the filamentous sulfide-oxidizing bacterium Thiothrix sp. (21).During a recent microbial survey of cold sulfidic springs in Bavaria, Germany, a second type of microbial string-of-pearls community was discovered in the streamlet of the "Islinger Mühlbach" (Regensburg, Southern Germany) (31). The SM1 euryarchaeon was again predominant in the pearl interior, while its partner was represented by the filamentous so-called IMB1 ε-proteobacterium, most probably outcompeting Thiothrix at the low in situ oxygen concentrations. The ...

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.

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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.

we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil 27 bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure 28 strains of methanotrophic bacteria, we assembled artificial communities of different diversity 29 levels, with which we inoculated sterile soil microcosms. To assess the functioning of these 30 communities, we measured methane oxidation by gas chromatography throughout the 31 experiment and determined changes in community composition and community size at several 32 time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a 33 positive overyielding-effect on methane oxidation, in particular at the beginning of the 34 experiment. This higher assimilation of CH 4 at high diversity translated into increased growth 35 and significantly larger communities towards the end of the study. The overyielding of mixtures 36 with respect to CH 4 consumption and community size was positively correlated. The temporal 37 CH 4 consumption profiles of strain monocultures differed, raising the possibility that temporal 38 complementarity of component strains drove the observed community-level strain richness 39 effects; however, the community niche metric we derived from the temporal activity profiles did 40 not explain the observed strain richness effect. The strain richness effect also was unrelated to 41 both the phylogenetic and functional trait diversity of mixed communities. Overall, our results 42 suggest that positive biodiversity-ecosystem function relationships show similar patterns across 43 different scales and may be widespread in nature. Additionally, biodiversity is probably also 44 important in natural methanotrophic communities for the ecosystem function methane oxidation. 45 3 Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help 46 to reduce the emission of the greenhouse gas methane. 47 48