Summary The effects of increased atmospheric nitrogen inputs, from both NOy and NHx, on diversity in various semi‐natural and natural ecosystems are reviewed. The severity of these impacts depends on abiotic conditions (e.g. buffering capacity, soil nutrient status and soil factors that influence the nitrification potential and nitrogen immobilization rate) in the particular system. The sensitivity of fresh water ecosystems, wetlands and bogs, species‐rich grasslands, heathlands and field layer of forests, all of which have conservational value, are discussed in detail. The most important effects of nitrogen deposition are: (i) accumulation of nitrogenous compounds resulting in enhanced availability of nitrate or ammonium; (ii) soil‐mediated effects of acidification; and (iii) increased susceptibility to secondary stress factors. Long‐term nitrogen enrichment has gradually increased the availability of nitrogen in several vegetation types, leading to competitive exclusion of characteristic species by more nitrophilic plants, especially under oligo‐ to mesotrophic soil conditions. Soil acidification (with losses of buffering capacity and increased concentrations of toxic metals) is especially important after nitrification of ammonium in weakly buffered environments: acid‐resistant plant species then become dominant at the expense of the often rare plants typical of intermediate pH. The related change in the balance between ammonium and nitrate may also affect the performance of several species. The susceptibility of plant species to secondary stress factors (pathogens; frost and drought) may be affected by air‐borne nitrogen but data are only available for a few communities (e.g. dry heathlands). Most global biodiversity is contained within natural and semi‐natural vegetation. It is thus crucial to control emissions of nitrogenous compounds to the atmosphere, in order to reduce or prevent effects on diversity in these systems. Most research has focused on acidification in forestry stands and lakes and on the effects on trees. We highlight serious gaps in knowledge of other ecosystems.

Wetlands are the largest natural source of atmospheric methane 1 , the second most important greenhouse gas 2 . Methane flux to the atmosphere depends strongly on the climate 3 ; however, by far the largest part of the methane formed in wetland ecosystems is recycled and does not reach the atmosphere 4,5 . The biogeochemical controls on the efficient oxidation of methane are still poorly understood. Here we show that submerged Sphagnum mosses, the dominant plants in some of these habitats, consume methane through symbiosis with partly endophytic methanotrophic bacteria, leading to highly effective in situ methane recycling. Molecular probes revealed the presence of the bacteria in the hyaline cells of the plant and on stem leaves. Incubation with 13 C-methane showed rapid in situ oxidation by these bacteria to carbon dioxide, which was subsequently fixed by Sphagnum, as shown by incorporation of 13 C-methane into plant sterols. In this way, methane acts as a significant (10-15%) carbon source for Sphagnum. The symbiosis explains both the efficient recycling of methane and the high organic carbon burial in these wetland ecosystems.Peat bogs alternate between lawns and pools. Lawns are dominated by species that grow up to several decimetres above the water table. Pools are dominated by aquatic species, such as Sphagnum cuspidatum, that form layers of living plants below the water table. We investigated the methane-oxidizing activity of submerged S. cuspidatum from peat bog pools at different field locations in the Netherlands, and compared it to the activity of S. magellanicum and S. papillosum growing in lawns. The potential methane-oxidizing activity was substantially higher in the submerged mosses (Fig. 1). In control experiments with bog water, methane was not oxidized, indicating that the methanotrophic bacteria were mainly present on or in the living Sphagnum tissue.The identity and location of these methanotrophs was determined in a molecular approach. Total genomic DNA from washed Sphagnum plants was isolated and bacterial 16S ribosomal RNA genes were amplified, cloned into Escherichia coli, sequenced and analysed phylogenetically. One of the 16S rRNA gene sequences of the clone library was affiliated to a cluster of type II methanotrophs that contained acidophilic methanotrophs isolated from Sphagnum bogs, such as Methylocella palustris (identity 93%) 6 and Methylocapsa acidiphila (identity 93%) 7 .The full 16S rRNA gene sequence was used to design two specific oligonucleotide probes for fluorescence in situ hybridization (FISH). FISH was combined with serial sectioning of the stems and the stem leaves of multiple individuals of submerged S. cuspidatum. The methanotrophic bacterium targeted by the probes was the dominant methanotroph in S. cuspidatum sections, accounting for over 75% of

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Summary Raised bogs are among the ecosystems most susceptible to atmospheric nitrogen pollution. Based on global data ranging from pristine to heavily polluted areas, a conceptual model is presented to explain the logistic response of these terrestrial carbon reservoirs to increased airborne nitrogen fluxes.

In recent decades, sulfate concentrations in many European freshwater wetlands have increased by 10-fold or more, due mainly to the use of sulfate-polluted river water to compensate for water shortage in these areas. To test the effect of sulfate enrichment, a mesocosm experiment was set up, using waterlogged soil cores, intact with vegetation, from a mesotrophic fen meadow. During sulfate addition at environmentally relevant levels (0, 2, and 4 mmol L -1 ), phosphate concentration and alkalinity of the pore water rapidly rose due to increased sulfate reduction rates. Free sulfide accumulated to levels toxic to several wetland plant species and biomass regrowth after harvesting was significantly lower on treated soils, especially for Carex species. Eventually, the concentrations of ammonium, phosphate, and potassium increased strongly in the treated soils due to reduced uptake by plants and extra mineralization. Sulfate availability was rate limiting, until the supply of readily decomposable organic matter became limited. It is argued that the significance of the observed changes in free sulfide concentrations and in the rate of nutrient mobilization should be recognized, and that these effects can be as important as direct eutrophication caused by the import of nutrients. The reported changes may severely influence the plant species composition of freshwater wetlands.

In wetland soils and underwater sediments of marine, brackish and freshwater systems, the strong phytotoxin sulfide may accumulate as a result of microbial reduction of sulfate during anaerobiosis, its level depending on prevailing edaphic conditions. In this review, we compare an extensive body of literature on phytotoxic effects of this reduced sulfur compound in different ecosystem types, and review the effects of sulfide at multiple ecosystem levels: the ecophysiological functioning of individual plants, plant-microbe associations, and community effects including competition and facilitation interactions. Recent publications on multi-species interactions in the rhizosphere show even more complex mechanisms explaining sulfide resistance. It is concluded that sulfide is a potent phytotoxin, profoundly affecting plant fitness and ecosystem functioning in the full range of wetland types including coastal systems, and at several levels. Traditional toxicity testing including hydroponic approaches generally neglect rhizospheric effects, which makes it difficult to extrapolate results to real ecosystem processes. To explain the differential effects of sulfide at the different organizational levels, profound knowledge about the biogeochemical, plant physiological and ecological rhizosphere processes is vital. This information is even more important, as anthropogenic inputs of sulfur into freshwater ecosystems and organic loads into freshwater and marine systems are still much higher than natural levels, and are steeply increasing in Asia. In addition, higher temperatures as a result of global climate change may lead to higher sulfide production rates in shallow waters.

Fens represent a large array of ecosystem services, including the highest biodiversity found among wetlands, hydrological services, water purification and carbon sequestration. Land-use change and drainage has severely damaged or annihilated these services in many parts of North America and Europe; restoration plans are urgently needed at the landscape level. We review the major constraints on the restoration of rich fens and fen water bodies in agricultural areas in Europe and disturbed landscapes in North America: (i) habitat quality problems: drought, eutrophication, acidification, and toxicity, and (ii) recolonization problems: species pools, ecosystem fragmentation and connectivity, genetic variability, and invasive species; and here provide possible solutions. We discuss both positive and negative consequences of restoration measures, and their causes. The restoration of wetland ecosystem functioning and services has, for a long time, been based on a trial-and-error approach. By presenting research and practice on the restoration of rich fen ecosystems within agricultural areas, we demonstrate the importance of biogeochemical and ecological knowledge at different spatial scales for the management and restoration of biodiversity, water quality, carbon sequestration and other ecosystem services, especially in a changing climate. We define target processes that enable scientists, nature managers, water managers and policy makers to choose between different measures and to predict restoration prospects for different types of deteriorated fens and their starting conditions.

One of the major threats to the structure and the functioning of natural and semi-natural ecosystems is the recent increase in airborne nitrogen pollution (NHy and NOx). Ecological effects of increased N supply are reviewed with respect to changes in vegetation and fauna in terrestrial and aquatic natural and semi-natural ecosystems. Observed and validated changes using data of field surveys, experimental studies or, of dynamic ecosystem models (the 'empirical approach'), are used as an indication for the impacts of N deposition. Based upon these data N critical loads are set with an indication of the reliability. Critical loads are given within a range per ecosystem, because of spatial differences in ecosystems. The following groups of ecosystems have been treated: softwater lakes, wetlands & bogs, species-rich grasslands, heathlands and forests. In this paper the effects of N deposition on softwater lakes have been discussed in detail and a summary of the N critical loads for all groups of ecosystems is presented. The nitrogen critical load for the most sensitive ecosystems (softwater lakes, ombrotrophic bogs) is between 5-10 kg N ha ~ y&, whereas a more average value for the range of studied ecosystems is 15-20 kg N ha-~ y&. Finally, major gaps in knowledge with respect to N critical loads are identified.