In the biogeochemical nitrogen cycle, microbial respiration processes compete for nitrate as an electron acceptor. Denitrification converts nitrate into nitrogenous gas and thus removes fixed nitrogen from the biosphere, whereas ammonification converts nitrate into ammonium, which is directly reusable by primary producers. We combined multiple parallel long-term incubations of marine microbial nitrate-respiring communities with isotope labeling and metagenomics to unravel how specific environmental conditions select for either process. Microbial generation time, supply of nitrite relative to nitrate, and the carbon/nitrogen ratio were identified as key environmental controls that determine whether nitrite will be reduced to nitrogenous gas or ammonium. Our results define the microbial ecophysiology of a biogeochemical feedback loop that is key to global change, eutrophication, and wastewater treatment.

/pdf/the-environmental-controls-that-govern-the-end-product-of-1c4utoy1jk.pdf

The environmental controls that govern the end product of bacterial nitrate respiration

Microbial nitrate respiration – Genes, enzymes and environmental distribution

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate (NO3-¬) and production of the potent greenhouse gas, nitrous oxide (N2O). A number of factors are known to control these processes, including O2 concentrations and moisture content, N, C, pH and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub cm areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location and potential for N2O production from soils.

/pdf/soil-nitrate-reducing-processes-drivers-mechanisms-for-3px2q1qlzz.pdf

Soil nitrate reducing processes drivers, mechanisms for spatial variation, and significance for nitrous oxide production

Anaerobic methane oxidation coupled to denitrification, also known as “nitrate/nitrite-dependent anaerobic methane oxidation” (n-damo), was discovered in 2006. Since then, only a few studies have identified this process and the associated microorganisms in natural environments. In aquatic sediments, the close proximity of oxygen- and nitrate-consumption zones can mask n-damo as aerobic methane oxidation. We therefore investigated the vertical distribution and the abundance of denitrifying methanotrophs related to Candidatus Methylomirabilis oxyfera with cultivation-independent molecular techniques in the sediments of Lake Constance. Additionally, the vertical distribution of methane oxidation and nitrate consumption zones was inferred from high-resolution microsensor profiles in undisturbed sediment cores. M. oxyfera-like bacteria were virtually absent at shallow-water sites (littoral sediment) and were very abundant at deep-water sites (profundal sediment). In profundal sediment, the vertical distribution of M. oxyfera-like bacteria showed a distinct peak in anoxic layers that coincided with the zone of methane oxidation and nitrate consumption, a strong indication for n-damo carried out by M. oxyfera-like bacteria. Both potential n-damo rates calculated from cell densities (660–4,890 µmol CH4⋅m−2⋅d−1) and actual rates calculated from microsensor profiles (31–437 µmol CH4⋅m−2⋅d−1) were sufficiently high to prevent methane release from profundal sediment solely by this process. Additionally, when nitrate was added to sediment cores exposed to anoxic conditions, the n-damo zone reestablished well below the sediment surface, completely preventing methane release from the sediment. We conclude that the previously overlooked n-damo process can be the major methane sink in stable freshwater environments if nitrate is available in anoxic zones.

/pdf/anaerobic-methane-oxidation-coupled-to-denitrification-is-j3olrdgnjc.pdf

Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are competing microbial nitrate-reduction processes. The occurrence of DNRA has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in a laboratory reactor, yet no successful DNRA enrichment culture has been described. We showed that a stable DNRA-dominated enrichment culture can be obtained in a chemostat system. The enrichment was based on the hypothesis that nitrate limitation is the dominant factor in selecting for DNRA. First, a conventional denitrifying culture was enriched from activated sludge, with acetate and nitrate as substrates. Next, the acetate concentration in the medium was increased to obtain nitrate-limiting conditions. As a result, conversions shifted from denitrification to DNRA. In this selection of a DNRA culture, two important factors were the nitrate limitation and a relatively low dilution rate (0.026 h−1). The culture was a highly enriched population of Deltaproteobacteria most closely related to Geobacter lovleyi, based on 16S rRNA gene sequencing (97% similarity). We established a stable and reproducible cultivation method for the enrichment of DNRA bacteria in a continuously operated reactor system. This enrichment method allows to further investigate the DNRA process and address the factors for competition between DNRA and denitrification, or other N-conversion pathways.

/pdf/enrichment-of-dnra-bacteria-in-a-continuous-culture-56ca3lw05r.pdf

Enrichment of DNRA bacteria in a continuous culture

The relative importance of two dissimilatory ni- trate reduction pathways, denitrification (DEN) and dissim- ilatory nitrate reduction to ammonium (DNRA), was inves- tigated in intact sediment cores from five different coastal marine field sites (Dorum, Aarhus Bight, Mississippi Delta, Limfjord and Janssand). The vertical distribution of DEN ac- tivity was examined using the acetylene inhibition technique combined with N2O microsensor measurements, whereas NH + production via DNRA was measured with a recently developed gel probe-stable isotope technique. At all field sites, dissimilatory nitrate reduction was clearly dominated by DEN (59-131 % of the total NO 3 reduced) rather than by DNRA, irrespective of the sedimentary inventories of elec- tron donors such as organic carbon, sulfide, and iron. High- est ammonium production via DNRA, accounting for up to 8.9 % of the total NO 3 reduced, was found at a site with very high concentrations of total sulfide and NH + within and be- low the layer in which NO 3 reduction occurred. Sediment from two field sites, one with low and one with high DNRA activity in the core incubations, was also used for slurry in- cubations. Now, in both sediments high DNRA activity was detected accounting for 37-77 % of the total NO 3 reduced. These contradictory results might be explained by enhanced NO 3 availability for DNRA bacteria in the sediment slurries compared to the core-incubated sediments in which diffusion of NO 3 from the water column may only reach DEN bac- teria, but not DNRA bacteria. The true partitioning of dis- similatory nitrate reduction between DNRA and DEN may thus lie in between the values found in whole core (under- estimation of DNRA) and slurry incubations (overestimation of DNRA).

/pdf/vertical-activity-distribution-of-dissimilatory-nitrate-3yfro2u0dw.pdf

Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments

Effect of high electron donor supply on dissimilatory nitrate reduction pathways in a bioreactor for nitrate removal

Dissimilatory NO3− reduction in sediments is often measured in bulk incubations that destroy in situ gradients of controlling factors such as sulfide and oxygen. Additionally, the use of unnaturally high NO3− concentrations yields potential rather than actual activities of dissimilatory NO3− reduction. We developed a technique to determine the vertical distribution of the net rates of dissimilatory nitrate reduction to ammonium (DNRA) with minimal physical disturbance in intact sediment cores at millimeter-level resolution. This allows DNRA activity to be directly linked to the microenvironmental conditions in the layer of NO3− consumption. The water column of the sediment core is amended with 15NO3− at the in situ 14NO3− concentration. A gel probe is deployed in the sediment and is retrieved after complete diffusive equilibration between the gel and the sediment pore water. The gel is then sliced and the NH4+ dissolved in the gel slices is chemically converted by hypobromite to N2 in reaction vials. The isotopic composition of N2 is determined by mass spectrometry. We used the combined gel probe and isotopic labeling technique with freshwater and marine sediment cores and with sterile quartz sand with artificial gradients of 15NH4+. The results were compared to the NH4+ microsensor profiles measured in freshwater sediment and quartz sand and to the N2O microsensor profiles measured in acetylene-amended sediments to trace denitrification.

/pdf/combined-gel-probe-and-isotope-labeling-technique-for-4gqoeajigw.pdf

Combined Gel Probe and Isotope Labeling Technique for Measuring Dissimilatory Nitrate Reduction to Ammonium in Sediments at Millimeter-Level Resolution

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Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments

Effect of high electron donor supply on dissimilatory nitrate reduction pathways in a bioreactor for nitrate removal

Combined Gel Probe and Isotope Labeling Technique for Measuring Dissimilatory Nitrate Reduction to Ammonium in Sediments at Millimeter-Level Resolution