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Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N 2 O - is intricately controlled by O 2 . While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N 2 O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O 2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O 2 legacy for accurately predicting N 2 O emissions originating from denitrification., (© 2024. The Author(s).)

Denitrifying bacteria have variable ability to perform efficient and balanced denitrification during oxygen depletion. NO is often assumed to exert a positive feedback in the transcription of denitrification genes, because NO-dependent activators have been identified. The regulatory network of denitrification is complex, however, and the significance of NO signalling needs to be studied in vivo. We utilized acetylene-catalysed NO oxidation to scavenge NO produced by batch cultures of denitrifying bacteria during transition from oxic to anoxic respiration, to explore the effects on the kinetics of NO, N(2) O and N(2) production. The results demonstrated that nanomolar concentrations of NO accumulating prior to complete depletion of oxygen exert a significant positive feedback on the initiation of denitrification in Paracoccus denitrificans. The early NO signal appeared essential to minimize the transient accumulation of NO during the subsequent anoxic phase for Agrobacterium tumefaciens, but not for P. denitrificans and Pseudomonas aureofaciens. In summary, the results indicate that the early accumulation of nanomolar concentrations of NO has a significant, but strain-dependent effect on the expression of denitrification., (© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Denitrifying prokaryotes are phylogenetically and functionally diverse. Little is known about the relationship between soil denitrifier community composition and functional traits. We extracted bacterial cells from three cultivated peat soils with contrasting native pH by density gradient centrifugation and investigated their kinetics of oxygen depletion and NO2 -, NO, N(2) O and N(2) accumulation during initially hypoxic batch incubations (0.5-1 μM O(2)) in minimal medium buffered at either pH 5.4 or 7.1 (2 mM glutamate, 2 mM NO3 -). The three communities differed strikingly in NO2 - accumulation and transient N(2) O accumulation at the two pH levels, whereas NO peak concentrations (24-53 nM) were similar across all communities and pH treatments. The results confirm that the communities represent different denitrification regulatory phenotypes, as indicated by previous denitrification bioassays with nonbuffered slurries of the same three soils. The composition of the extracted cells resembled that of the parent soils (PCR-TRFLP analyses of 16S rRNA genes, nirK, nirS and nosZ), which were found to differ profoundly in their genetic composition (Braker et al., ). Together, this suggests that direct pH response of denitrification depends on denitrifier community composition, with implications for the propensity of soils to emit N(2) O to the atmosphere., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes (DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N(2) O/N(2) ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes (nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N(2) O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N(2) O/N(2) ) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N(2) O/N(2) ). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N(2) O emission of the soils., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Little is known about the genetic and phenotypic diversity of Gram-positive denitrifying bacteria. We compared the production of gaseous denitrification products for 14 closely related Bacillus soil isolates at pH 6 and 7 during 48-h batch incubations using a robotic gas-sampling apparatus. Primers targeting the nosZ gene encoding the nitrous oxide reductase were designed to confirm the presence of this gene in the isolates. The variation in the production of gaseous nitrogen products was compared with the genetic variation based on 16S rRNA gene sequences, genomic fingerprinting and nosZ sequences. The nosZ gene was detected in all isolates and all produced N(2) as the dominant end product at pH 7. Production of gaseous nitrogen products was more variable at pH 6, with different levels of NO and N(2) O production among the isolates, although minimal variation was observed among the 16S rRNA and nosZ gene sequences. One isolate was more divergent from the others based on genomic fingerprinting, and had two different nosZ gene copies, which coincided with the highest production of N(2) at pH 7 and the lack of intermediates at pH 6. Overall, our analysis suggests that genetic variation plays a role in the variation in N(2) O and N(2) production, but the variation in activity caused by acidification can be substantially greater than genotypic variation among closely related Bacillus., (© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Abstract Biogeochemical models simulate soil nitrogen (N) turnover and are often used to assess N losses through denitrification. Though models simulate a complete N budget, often only a subset of N pools/fluxes (i.e., N2O, NO3−, NH3, NOx) are published since the full budget cannot be validated with measured data. Field studies rarely include full N balances, especially N2 fluxes, which are difficult to quantify. Limiting publication of modeling results based on available field data represents a missed opportunity to improve the understanding of modeled processes. We propose that the modeler community support publication of all simulated N pools and processes in future studies.