Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

We have studied the distribution and community composition of denitrifying bacteria in the stratified water column and at the sediment–water interface in lakes Plußsee and Schöhsee, and a near-shore site in the Baltic Sea in Germany. Although environmental changes induced by the stratification of the water column in marine environments are known to affect specific populations of denitrifying bacteria, little information is available for stratified freshwater lakes and brackish water. The aim of the present study was to fill this gap and to demonstrate specific distribution patterns of denitrifying bacteria in specific aquatic habitats using two functional markers for the nitrite reductase (nirK and nirS genes) as a proxy for the communities. The leading question to be answered was whether communities containing the genes nirK and nirS have similar, identical, or different distribution patterns, and occupy the same or different ecological niches. The genes nirK and nirS were analyzed by PCR amplification with specific primers followed by terminal restriction fragment length polymorphism (T-RFLP) and by cloning and sequence analysis. Overall, nirS-denitrifiers were more diverse than nirK-denitrifiers. Denitrifying communities in sediments were clearly different from those in the water column in all aquatic systems, regardless of the gene analyzed. A differential distribution of denitrifying assemblages was observed for each particular site. In the Baltic Sea and Lake Plußsee, nirK-denitrifiers were more diverse throughout the water column, while nirS-denitrifiers were more diverse in the sediment. In Lake Schöhsee, nirS-denitrifiers showed high diversity across the whole water body. Habitat-specific clusters of nirS sequences were observed for the freshwater lakes, while nirK sequences from both freshwater lakes and the Baltic Sea were found in common phylogenetic clusters. These results demonstrated differences in the distribution of bacteria containing nirS and those containing nirK indicating that both types of denitrifiers apparently occupy different ecological niches

Identification and isolation of active N2O reducers in rice paddy soil

Dissolved N2O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N2O is emitted to the atmosphere above these fields. This indicates the occurrence of N2O reduction in rice paddy fields; however, identity of the N2O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N2O reducers in rice paddy soil. In a soil microcosm, N2O and succinate were added as the electron acceptor and donor, respectively, for N2O reduction. For the stable isotope probing (SIP) experiment, 13C-labeled succinate was used to identify succinate-assimilating microbes under N2O-reducing conditions. DNA was extracted 24 h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N2O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N2O-reducing conditions in the presence of cell division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N2O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N2O-reducing conditions, in contrast to the control sample (soil incubated with only 13C-succinate added). Results of the single-cell isolation technique also indicated that the majority of the N2O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N2O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N2O reduction in rice paddy soils

Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment

International audienceThe relative importance of size and composition of microbial communities in ecosystem functioning is poorly understood. Here, we investigated how community composition and size of selected functional guilds in the nitrogen cycle correlated with agroecosystem functioning, which was defined as microbial process rates, total crop yield and nitrogen content in the crop. Soil was sampled from a 50-year fertilizer trial and the treatments comprised unfertilized bare fallow, unfertilized with crop, and plots with crop fertilized with calcium nitrate, ammonium sulfate, solid cattle manure or sewage sludge. The size of the functional guilds and the total bacterial community were greatly affected by the fertilization regimes, especially by the sewage sludge and ammonium sulfate treatments. The community size results were combined with previously published data on the composition of the corresponding communities, potential ammonia oxidation, denitrification, basal and substrate-induced respiration rates, in addition to crop yield for an integrated analysis. It was found that differences in size, rather than composition, correlated with differences in process rates for the denitrifier and ammonia-oxidizing archaeal and total bacterial communities, whereas neither differences in size nor composition was correlated with differences in process rates for the ammonia-oxidizing bacterial community. In contrast, the composition of nitrate-reducing, denitrifying and total bacterial communities co-varied with primary production and both were strongly linked to soil properties