Summary This paper reports the range and statistical distribution of oxidation rates of atmospheric CH4 in soils found in Northern Europe in an international study, and compares them with published data for various other ecosystems. It reassesses the size, and the uncertainty in, the global terrestrial CH4 sink, and examines the effect of land‐use change and other factors on the oxidation rate. Only soils with a very high water table were sources of CH4; all others were sinks. Oxidation rates varied from 1 to nearly 200 μg CH4 m−2 h−1; annual rates for sites measured for ≥1 y were 0.1–9.1 kg CH4 ha−1 y−1, with a log‐normal distribution (log‐mean ≈ 1.6 kg CH4 ha−1 y−1). Conversion of natural soils to agriculture reduced oxidation rates by two‐thirds –‐ closely similar to results reported for other regions. N inputs also decreased oxidation rates. Full recovery of rates after these disturbances takes > 100 y. Soil bulk density, water content and gas diffusivity had major impacts on oxidation rates. Trends were similar to those derived from other published work. Increasing acidity reduced oxidation, partially but not wholly explained by poor diffusion through litter layers which did not themselves contribute to the oxidation. The effect of temperature was small, attributed to substrate limitation and low atmospheric concentration. Analysis of all available data for CH4 oxidation rates in situ showed similar log‐normal distributions to those obtained for our results, with generally little difference between different natural ecosystems, or between short‐and longer‐term studies. The overall global terrestrial sink was estimated at 29 Tg CH4 y−1, close to the current IPCC assessment, but with a much wider uncertainty range (7 to > 100 Tg CH4 y−1). Little or no information is available for many major ecosystems; these should receive high priority in future research.

Field-scale experiments simulating realistic future climate scenarios are important tools for investigating the effects of current and future climate changes on ecosystem functioning and biogeochemical cycling. We exposed a seminatural Danish heathland ecosystem to elevated atmospheric carbon dioxide (CO 2 ), warming, and extended summer drought in all combinations. Here, we report on the short-term responses of the nitrogen (N) cycle after 2 years of treatments. Elevated CO 2 significantly affected aboveground stoichiometry by increasing the carbon to nitrogen (C/N) ratios in the leaves of both co-dominant species (Calluna vulgaris and Deschampsia flexuosa), as well as the C/N ratios of Calluna flowers and by reducing the N concentration of Deschampsia litter. Belowground, elevated CO 2 had only minor effects, whereas warming increased N turnover, as indicated by increased rates of microbial NH 4 1 consumption, gross mineralization, potential nitrification, denitrification and N 2 O emissions. Drought reduced belowground gross N mineralization and decreased fauna N mass and fauna N mineralization. Leaching was unaffected by treatments but was significantly higher across all treatments in the second year than in the much drier first year indicating that ecosystem N loss is highly sensitive to changes and variability in amount and timing of precipitation. Interactions between treatments were common and although some synergistic effects were observed, antagonism dominated the interactive responses in treatment combinations, i.e. responses were smaller in combinations than in single treatments. Nonetheless, increased C/N ratios of photosynthetic tissue in response to elevated CO 2 , as well as drought-induced decreases in litter N production and fauna N mineralization prevailed in the full treatment combination. Overall, the simulated future climate scenario therefore lead to reduced N turnover, which could act to reduce the potential growth response of plants to elevated atmospheric CO 2 concentration.

The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one pattern was found in both soils and in each soil two dominant groups comprised >35% of all clones. No dominance and few redundant patterns were seen among the nirS clones. Phylogenetic analysis of deduced amino acids grouped the nirK sequences into five major clusters, with one cluster encompassing most marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall, the data indicated that the denitrifying communities in the two soils have many members and that the soils have a high richness of different nir genes, especially of the nirS gene, most of which have not yet been found in cultivated denitrifiers.

Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism (pathogen)-independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduct of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.

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