The oxidation of methane by methane-oxidising microorganisms is an important link in the global methane budget. Oxic soils are a net sink while wetland soils are a net source of atmospheric methane. It has generally been accepted that the consumption of methane in upland as well as lowland systems is inhibited by nitrogenous fertiliser additions. Hence, mineral nitrogen (i.e. ammonium/nitrate) has conceptually been treated as a component with the potential to enhance emission of methane from soils and sediments to the atmosphere, and results from numerous studies have been interpreted as such. Recently, ammonium-based fertilisation was demonstrated to stimulate methane consumption in rice paddies. Growth and activity of methane-consuming bacteria in microcosms as well as in natural rice paddies was N limited. Analysing the available literature revealed that indications for N limitation of methane consumption have been reported in a variety of lowland soils, upland soils, and sediments. Obviously, depriving methane-oxidising bacteria of a suitable source of N hampers their growth and activity. However, an almost instantaneous link between the presence of mineral nitrogen (i.e. ammonium, nitrate) and methane-oxidising activity, as found in rice soils and culture experiments, requires an alternative explanation. We propose that switching from mineral N assimilation to the fixation of molecular nitrogen may explain this phenomenon. However, there is as yet no experimental evidence for any mechanism of instantaneous stimulation, since most studies have assumed that nitrogenous fertiliser is inhibitory of methane oxidation in soils and have focused only on this aspect. Nitrogen as essential factor on the sink side of the global methane budget has been neglected, leading to erroneous interpretation of methane emission dynamics, especially from wetland environments. The purpose of this minireview is to summarise and balance the data on the regulatory role of nitrogen in the consumption of methane by soils and sediments, and thereby stimulate the scientific community to embark on experiments to close the existing gap in knowledge. ß 2004 Published by Elsevier B.V. on behalf of the Federation of European Microbiological Societies.

The role of the nitrogen cycle in repression of methane production is probably low. In contrast to wetlands particularly created for the purification of nitrogen-rich waste waters, concentrations of inorganic nitrogen compounds are low in the root zones in the growing season due to the nitrogen-consuming behaviour of the plant. Therefore, nitrate hardly competes with other electron acceptors for reduced organic compounds, and repression of methane oxidation by the presence of higher levels of ammonium will not be the case. The role of the iron cycle is likely to be important with respect to the repression of methane production and oxidation. Iron-reducing and iron-oxidizing bacteria are ubiquitous in the rhizosphere of wetland plants. The cycling of iron will be largely dependent on the size of the oxygen release in the root zone, which is likely to be different between different wetland plant species. The role of the sulfur cycle in repression of methane production is important in marine, sulfate-rich ecosystems, but might also play a role in freshwater systems where sufficient sulfate is available. Sulfate-reducing bacteria are omnipresent in freshwater ecosystems, but do not always react immediately to the supply of fresh sulfate. Hence, their role in the repression of methanogenesis is still to be proven in freshwater marshes.

A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a mutational hot spot, and cloning of heteroduplexes and chimeras. These data may partially explain the high degree of microheterogeneity typical of sequence clusters detected in environmental clone libraries.

In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 M ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.

Colony counts of acetate-, propionate- and L-lactate-oxidizing sulfate-reducing bacteria in marine sediments were made. The vertical distribution of these organisms were equal for the three types considered. The highest numbers were found just beneath the border of aerobic and anaerobic layers. Anaerobic mineralization of acetate, propionate and L-lactate was studied in the presence and in the absence of sulfate. In freshwater and in marine sediments, acetate and propionate were oxidized completely with concomitant reduction of sulfate. L-Lactate was always fermented. Lactate-oxidizing, sulfate-reducing bacteria could only be isolated from marine sediments, they belonged to the genus Desulfobacter and oxidized only acetate and ethanol by sulfate reduction. Propionate-oxidizing, sulfate-reducing bacteria belonged to the genus Desulfobulbus. They were isolated from freshwater as well as from marine sediments and showed a relatively large range of usable substrates: hydrogen, formate, propionate, L-lactate and ethanol were oxidized with concomitant sulfate reduction. L-Lactate and pyruvate could be fermented by most of the isolated strains.

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Abstract. To prevent flooding of the Dutch delta, former estuaries have been impounded by the building of dams and sluices. Some of these water bodies, however, experience major ecological problems. One of the problem areas is the former Volkerak estuary that was turned into a freshwater lake in 1987. From the early 1990s onward, toxic Microcystis blooms dominate the phytoplankton of the lake every summer. Two management strategies have been suggested to suppress these harmful algal blooms: flushing the lake with fresh water or reintroducing saline water into the lake. This study aims at an advance assessment of these strategies through the development of a mechanistic model of the population dynamics of Microcystis. To calibrate the model, we monitored the benthic and pelagic Microcystis populations in the lake during two years. Field samples of Microcystis were incubated in the laboratory to estimate growth and mortality rates as functions of light, temperature, and salinity. Recruitment and sedimentation rates were measured in the lake, using traps, to quantify benthic-pelagic coupling of the Microcystis populations. The model predicts that flushing with fresh water will suppress Microcystis blooms when the current flushing rate is sufficiently increased. Furthermore, the inlet of saline water will suppress Microcystis blooms for salinities exceeding 14 g/L. Both management options are technically feasible. Our study illustrates that quantitative ecological knowledge can be a helpful tool guiding large-scale water management.

The community structure of ammonia-oxidizing bacteria of the β-subclass Proteobacteria was investigated with respect to environmental gradients along the Schelde, a eutrophic estuary system. A dominance of Nitrosomonas-like sequences was detected using molecular techniques targeting the 16S rRNA gene on 3 separate sampling dates, and different Nitrosomonas-like populations were most dominant at different locations along the estuary. The most frequently detected ammonia oxidizer-like sequences in the freshwater part of the estuary were associated with a sequence cluster previously designated as Nitrosomonas Cluster 6a. This group, which is closely affiliated with the cultured species N. ureae, has previously been detected as the dominant ammonia-oxidizer group in various freshwater systems, and was also the dominant recovered sequence cluster from a contributory, untreated sewage effluent sample. The 16S rDNA recovered from brackish locations further downstream was dominated by a group of novel Nitrosomonas-like sequences. Nitrosospira-like sequences represented only a small minority of those detected for all samples. The shift in dominant ammonia-oxidizer populations occurred in the estuarine region with the sharpest observed gradients in salinity, oxygen, and ammonia. These results provide evidence in support of the differential selection of physiologically distinct Nitrosomonas-like groups according to the environmental gradients encountered along the estuary KEY WORDS: Ammonia-oxidizing bacteria · Estuaries · DGGE · Nitrosomonas Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 23: [225][226][227][228][229][230][231][232][233][234][235][236] 2001 ents of salinity, ammonia concentration, and dissolved oxygen levels. Thus, as bacteria travel with the residual seaward current, they encounter changing environmental conditions. The residence time of water in the total estuary is about 60 d (Soetaert & Herman 1995b), although this may be extended by attachment to particles or by (temporary) sedimentation (Owens 1986). The mean residence time of particles in one compartment of the estuary (see Fig. 1) is comparable with the generation time of many cultured ammonia-oxidizing bacteria (Helder & de Vries 1983). Thus, competition and selection may occur between distinct ammonia-oxidizer populations as they travel through the Schelde estuary. Alternatively, ammonia-oxidizing bacteria may possess the ability to adapt to the environmental gradients encountered. Clues as to which of these processes most affect ammonia-oxidizer populations might therefore be gained by examining their community structure along the estuarine region where these key environmental gradients are observed.Ecological studies of ammonia-oxidizing bacteria have been hampered by the difficulties and biases associated with the isolation and manipulation of these organisms in pure culture (Koops & Harms 1985, Prosser 1989. The monophyletic nature of the β-subclass ammonia-oxidizing bacteria has h...