Owing to the present global biodiversity crisis, the biodiversity-stability relationship and the effect of biodiversity on ecosystem functioning have become major topics in ecology. Biodiversity is a complex term that includes taxonomic, functional, spatial and temporal aspects of organismic diversity, with species richness (the number of species) and evenness (the relative abundance of species) considered among the most important measures. With few exceptions (see, for example, ref. 6), the majority of studies of biodiversity-functioning and biodiversity-stability theory have predominantly examined richness. Here we show, using microbial microcosms, that initial community evenness is a key factor in preserving the functional stability of an ecosystem. Using experimental manipulations of both richness and initial evenness in microcosms with denitrifying bacterial communities, we found that the stability of the net ecosystem denitrification in the face of salinity stress was strongly influenced by the initial evenness of the community. Therefore, when communities are highly uneven, or there is extreme dominance by one or a few species, their functioning is less resistant to environmental stress. Further unravelling how evenness influences ecosystem processes in natural and humanized environments constitutes a major future conceptual challenge.

SummaryCommunity-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), singlestrand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a settingindependent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.

For more than 100 years it was believed that bacteria were the only group responsible for the oxidation of ammonia. However, recently, a new strain of archaea bearing a putative ammonia monooxygenase subunit A (amoA) gene and able to oxidize ammonia was isolated from a marine aquarium tank. Ammonia-oxidizing archaea (AOA) were subsequently discovered in many ecosystems of varied characteristics and even found as the predominant causal organisms in some environments. Here, we summarize the current knowledge on the environmental conditions related to the presence of AOA and discuss the possible site-related properties. Considering these data, we deduct the possible niches of AOA based on pH, sulfide and phosphate levels. It is proposed that the AOA might be important actors within the nitrogen cycle in low-nutrient, low-pH, and sulfide-containing environments.

A sequential batch reactor (SBR) and a membrane bioreactor (MBR) were inoculated with the same sludge from a municipal wastewater treatment plant, supplemented with ammonium, and operated in parallel for 84 days. It was investigated whether the functional stability of the nitrification process corresponded with a static ammonia-oxidizing bacterial (AOB) community. The SBR provided complete nitrification during nearly the whole experimental run, whereas the MBR showed a buildup of 0 to 2 mg nitrite-N liter ؊1 from day 45 until day 84. Based on the denaturing gradient gel electrophoresis profiles, two novel approaches were introduced to characterize and quantify the community dynamics and interspecies abundance ratios: (i) the rate of change [⌬ t(week) ] parameter and (ii) the Pareto-Lorenz curve distribution pattern. During the whole sampling period, it was observed that neither of the reactor types maintained a static microbial community and that the SBR evolved more gradually than the MBR, particularly with respect to AOB (i.e., average weekly community changes of 12.6% ؎ 5.2% for the SBR and 24.6% ؎ 14.3% for the MBR). Based on the Pareto-Lorenz curves, it was observed that only a small group of AOB species played a numerically dominant role in the nitritation of both reactors, and this was true especially for the MBR. The remaining less dominant species were speculated to constitute a reserve of AOB which can proliferate to replace the dominant species. The value of these parameters in terms of tools to assist the operation of activated-sludge systems is discussed. Fernandez et al. (12) demonstrated that ecosystem stability encompasses a broad spectrum of definitions. These definitions resolve into two components: the measurable functional properties of the ecosystem and the change over time of the community composition. Frequently, only the functional parameters are evaluated (37), but recently attempts were made to relate (dys)functioning with the structure of a microbial community (13,25,46,49). It was found that highly dynamic communities can still maintain a stable ecosystem function (12, 25).Curtis and Sloan (8) postulated that the relationship between structure and function in a microbial community can be evaluated only through an understanding of the source of diversity from which the community is drawn, named the global reservoir or metacommunity. Up to now, diversity has been mainly measured statically, based on indices such as Shannon and Simpson indices. By adding Lorenz curves, a nonambiguous graphical presentation of species evenness can be provided (31,35,42), investigating interspecies abundance ratios and thus the internal community structure. Besides the importance of the community diversity and composition at one time point, the dynamics of microbial communities can play an important role in the functionality of a system (49). Nevertheless, due to infrequent sampling, the dynamics of functionally stable microbial communities has not yet been quantified in terms of a rate of change on a sho...

An evolutionary algorithm was applied to study the complex interactions between medium parameters and their effects on the isolation of denitrifying bacteria, both in number and in diversity. Growth media with a pH of 7 and a nitrogen concentration of 3 mM, supplemented with 1 ml of vitamin solution but not with sodium chloride or riboflavin, were the most successful for the isolation of denitrifiers from activated sludge. The use of ethanol or succinate as a carbon source and a molar C/N ratio of 2.5, 20, or 25 were also favorable. After testing of 60 different medium parameter combinations and comparison with each other as well as with the standard medium Trypticase soy agar supplemented with nitrate, three growth media were highly suitable for the cultivation of denitrifying bacteria. All evaluated isolation conditions were used to study the cultivable denitrifier diversity of activated sludge from a municipal wastewater treatment plant. One hundred ninety-nine denitrifiers were isolated, the majority of which belonged to the Betaproteobacteria (50.4%) and the Alphaproteobacteria (36.8%). Representatives of Gammaproteobacteria (5.6%), Epsilonproteobacteria (2%), and Firmicutes (4%) and one isolate of the Bacteroidetes were also found. This study revealed a much more diverse denitrifying community than that previously described in cultivation-dependent research on activated sludge.For nearly 2 decades, molecular biology has provided the tools to successfully overcome the "great plate count anomaly" and allow the study of uncultured microbial diversity (3). The growing awareness that molecular methods cannot or, in very few cases, can only indirectly investigate the function of specific microorganisms in the environment has raised interest in new cultivation efforts and approaches once again (14,15,34). Simple adjustments to the classical cultivation approach, such as prolonging the incubation time and avoiding complex or nutrient-rich growth media, have successfully resulted in cultivation of previously uncultured bacteria (12,30).A physiological trait such as denitrification, the respiratory reduction of nitrate and nitrite to N 2 O and nitrogen gas, is not limited to specific microbial taxa and is therefore studied independent of culture through the relevant functional genes (6,25,32,38). To date, however, it is not clear to what extent, if at all, these functional genes contain phylogenetic information. Phillipot (22) showed that the phylogeny of nir and nor genes, coding for the key enzymes nitrite reductase and NO reductase in the denitrification pathway, does not always agree with the phylogeny of the 16S rRNA gene. New isolation and cultivation approaches are therefore imperative to provide the basis for further research on phylogenetic and functional gene diversity.The isolation of specific physiological groups of bacteria, such as denitrifiers, requires knowledge of the interactions of a large number of medium components and growth conditions. Genetic or evolutionary algorithms (EAs) are heuristic op...