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Concept: Denitrification


Agricultural soils represent the main source of anthropogenic N2O emissions. Recently, interactions of black carbon with the nitrogen cycle have been recognized and the use of biochar is being investigated as a means to reduce N2O emissions. However, the mechanisms of reduction remain unclear. Here we demonstrate the significant impact of biochar on denitrification, with a consistent decrease in N2O emissions by 10-90% in 14 different agricultural soils. Using the (15)N gas-flux method we observed a consistent reduction of the N2O/(N2 + N2O) ratio, which demonstrates that biochar facilitates the last step of denitrification. Biochar acid buffer capacity was identified as an important aspect for mitigation that was not primarily caused by a pH shift in soil. We propose the function of biochar as an “electron shuttle” that facilitates the transfer of electrons to soil denitrifying microorganisms, which together with its liming effect would promote the reduction of N2O to N2.

Concepts: Carbon dioxide, Metabolism, Nitrogen, PH, Buffer solution, Bioremediation, Denitrification, Nitrogen cycle


A major challenge for the bioremediation of toxic metals is the co-occurrence of nitrate, as it can inhibit metal transformation. Geobacter metallireducens, Desulfovibrio desulfuricans, and Sulfurospirillum barnesii are three soil bacteria that can reduce chromate [Cr(VI)] and nitrate, and may be beneficial for developing bioremediation strategies. All three organisms respire through dissimilatory nitrate reduction to ammonia (DNRA), employing different nitrate reductases but similar nitrite reductase (Nrf). G. metallireducens reduces nitrate to nitrite via the membrane bound nitrate reductase (Nar), while S. barnesii and D. desulfuricans strain 27774 have slightly different forms of periplasmic nitrate reductase (Nap). We investigated the effect of DNRA growth in the presence of Cr(VI) in these three organisms and the ability of each to reduce Cr(VI) to Cr(III), and found that each organisms responded differently. Growth of G. metallireducens on nitrate was completely inhibited by Cr(VI). Cultures of D. desulfuricans on nitrate media was initially delayed (48 h) in the presence of Cr(VI), but ultimately reached comparable cell yields to the non-treated control. This prolonged lag phase accompanied the transformation of Cr(VI) to Cr(III). Viable G. metallireducens cells could reduce Cr(VI), whereas Cr(VI) reduction by D. desulfuricans during growth, was mediated by a filterable and heat stable extracellular metabolite. S. barnesii growth on nitrate was not affected by Cr(VI), and Cr(VI) was reduced to Cr(III). However, Cr(VI) reduction activity in S. barnesii, was detected in both the cell free spent medium and cells, indicating both extracellular and cell associated mechanisms. Taken together, these results have demonstrated that Cr(VI) affects DNRA in the three organisms differently, and that each have a unique mechanism for Cr(VI) reduction.

Concepts: Bacteria, Metabolism, Redox, Nitrogen, Bioremediation, Denitrification, Nitrate, Nitrate reductase


Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially-mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups contributing to nitrogen cycling and a reproducible network of decomposers that emerge on predictable timescales. The results show this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development and the process of decomposition is sufficiently reproducible that it offers unique opportunities for forensic investigations.

Concepts: Oxygen, Bacteria, Metabolism, Enzyme, Nitrogen, Denitrification, Embalming, Nitrogen cycle


Distribution variation of a metabolic uncoupler, 2,6-dichlorophenol (2,6-DCP), in long-term sludge culture was studied, and the effects on sludge reduction and biological inhibition of this chemical during the 90-day operation were established. The extracellular polymeric substance (EPS) matrix functioned as a protective barrier for the bacteria inside sludge flocs to 2,6-DCP, resulting in the transfer of 2,6-DCP from the liquid phase to the activated sludge fraction. Significant sludge reduction (about 40%) was observed after the addition of 2,6-DCP in the first 40 days, while the ineffective function of 2,6-DCP in sludge reduction (days 70-90) might be correlated to the EPS protection mechanism. The inhibitory effect of 2,6-DCP on the COD removal was extremely lower than on the nitrification performance due to the fact that 2,6-DCP was much more toxic to autotrophic microorganisms than heterotrophic microorganisms. Moreover, both of them recovered to a higher level again with the transfer potential of 2,6-DCP to sludge. Thus, the application of metabolic uncoupler for excess sludge reduction should be cautious.

Concepts: DNA, Photosynthesis, Bacteria, Evolution, Organism, Microbiology, Denitrification, Primary nutritional groups


Water shortages and the drive to recycle is increasing interest in reuse of reclaimed wastewater. Timely and cost-effective ways to detect fecal pollutants prior to reuse increases confidence of residents and neighbors concerned about reuse of reclaimed wastewater. The on-site wastewater treatment and reuse systems (OWTRS) used in this study include a septic tank, peat bioreactor, ClO(2) disinfection and land spray irrigation system. Bacteroides fragilis, Escherichiacoli and Enterococcus spp., were tested with immunomagnetic separation/ATP bioluminescence (IMS/ATP), qPCR and culture-based methods. The results displayed a 2-log reduction in fecal bacteria in the peat bioreactor and a 5-log reduction following chloride dioxide disinfection. The fecal bacteria levels measured by IMS/ATP correlated with qPCR results: HuBac 16S (R(2) = 0.903), Bf-group 16S (R(2) = 0.956), gyrB (R(2) = 0.673), and Ent 23S (R(2) = 0.724). This is the first study in which the newly developed human-specific IMS/ATP and previously developed IMS/ATP were applied for determining OWTRS efficiency. Results of the study revealed that IMS/ATP is a timely and cost-effective way to detect fecal contaminants, and results were validated with qPCR and culture based methods. The new IMS/ATP can also be applied broadly in the detection of human-originated fecal contamination.

Concepts: Bacteria, Gut flora, Sewage treatment, Wastewater, Denitrification, Reclaimed water, Septic tank, Greywater


This study attempts to elucidate the emission sources and mechanisms of nitrous oxide (N2O) during simultaneous nitrification and denitrification (SND) process under oxygen-limiting condition. The results indicated that N2O emitted during low-oxygen SND process was 0.8±0.1mgN/gMLSS, accounting for 7.7% of the nitrogen input. This was much higher than the reported results from conventional nitrification and denitrification processes. Batch experiments revealed that nitrifier denitrification was attributed as the dominant source of N2O production. This could be well explained by the change of ammonia-oxidizing bacteria (AOB) community caused by the low-oxygen condition. It was observed that during the low-oxygen SND process, AOB species capable of denitrification, i.e., Nitrosomonas europaea and Nitrosomonas-like, were enriched whilst the composition of denitrifiers was only slightly affected. N2O emission by heterotrophic denitrification was considered to be limited by the presence of oxygen and unavailability of carbon source.

Concepts: Oxygen, Carbon dioxide, Bacteria, Nitrogen, Nitrous oxide, Denitrification, Nitrogen dioxide, Nitrogen cycle


Soil microbial community composition and activity could be affected by suitable manipulation of the environment they live in. If correctly applied such an approach could become a very effective way to remediate excess of chemicals. The concentration of nitrogen, especially nitrate deriving from agricultural managements, is generally found to increase in water flow. Therefore, by forcing the water flow through a buffer strip specifically designed and possibly afforested with suitable plant species, may result effective in reducing high nitrogen contents. The management of a riparian buffer may definitely affect the soil microbial activities, including denitrification, as well as the composition of the community. The present study reports on the changes occurred in terms of denitrifying microbial community composition, as compared to that of a neighbouring agricultural area, as a consequence of hydraulic management coupled to the suspension of farming practices and to the development of the woody and herbaceous vegetation. With this aim, denitrification was repeatedly measured and the data obtained were related to those deriving from a specific analysis of bacterial groups involved in denitrification. nirK, encoding for nitrite reductase, an enzyme essential for the conversion of nitrite to nitric oxide and considered the key step in the denitrification process, was chosen as the target gene. The main results obtained indicated that denitrification activity changes in riparian buffer as compared to agricultural soil and it is strongly influenced by carbon availability and soil depth. Although no significant differences on the community composition between superficial (0-15cm) and medium (40-55cm) layers were observed, the nirK-type denitrifier community was shown to significantly differ between riparian and agricultural soils in both surface and medium layers.

Concepts: Bacteria, Agriculture, Redox, Water pollution, Soil, Nitrogen, Denitrification, Agricultural soil science


Graphene oxide (GO) was applied in this study to enhance the activity of anaerobic ammonium oxidation (anammox) bacteria for nitrogen removal. A GO dose-dependent effect on anammox bacteria was observed through batch tests. The results showed that the activity increased as the GO dose was varied within 0.05-0.1gL. A maximum 10.26% increase of anaerobic ammonium oxidizing activity was achieved at 0.1gL GO. Analysis of extracellular polymeric substances (EPS) indicated that the highest carbohydrate, protein, and total EPS contents (42.5, 125.7, and 168.2mg (g volatile suspended solids), respectively) were obtained with 0.1gL GO. Appropriate GO dose stimulated EPS production to promote the activity of anammox bacteria. Transmission electron microscopy showed the large surface area of GO benefited cell attachment. These findings proved that the application of GO was an effective approach to enhancing the activity of anammox bacteria.

Concepts: Photosynthesis, Protein, Electron, Oxygen, Carbon dioxide, Nitrogen, Oxide, Denitrification


In marine ecosystems, both nitrite-reducing bacteria and anaerobic ammonium-oxidizing (anammox) bacteria, containing different types of NO-forming nitrite reductase-encoding genes, contribute to the nitrogen cycle. The objectives of study were to reveal the diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface environments. Results showed that higher diversity and abundance of nirS gene than nirK and Scalindua-nirS genes were evident in the sediments of the South China Sea (SCS), indicating bacteria containing nirS gene dominated the NO-forming nitrite-reducing microbial community in this ecosystem. Similar diversity and abundance distribution patterns of both nirS and Scalindua-nirS genes were detected in this study sites, but different from nirK gene. Further statistical analyses also showed both nirS and Scalindua-nirS genes respond similarly to environmental factors, but differed from nirK gene. These results suggest that bacteria containing nirS and Scalindua-nirS genes share similar niche in deep-sea subsurface sediments of the SCS, but differed from those containing nirK gene, indicating that community structures of nitrite-reducing bacteria are segregated by the functional modules (NirS vs. NirK) rather than the competing processes (anammox vs. classical denitrification).

Concepts: Archaea, Bacteria, Evolution, Metabolism, Organism, Nitrogen, South China Sea, Denitrification


The intensive application of fertilizers during agricultural practices has led to an unprecedented perturbation of the nitrogen cycle, illustrated by the growing accumulation of nitrates in soils and waters, and of nitrogen oxides in the atmosphere. Besides increasing use efficiency of current N fertilizers, priority should be given to put on value the process of biological nitrogen fixation, through more sustainable technologies that reduce the undesired effects of chemical N fertilization of agricultural crops. Wider legume adoption, supported by coordinated legume breeding and inoculation programs are approaches at hand. Also available are biofertilizers based on microbes that help to reduce the needs of N fertilization in important crops like cereals. Engineering in cereals the capacity to fix nitrogen, either by themselves or in symbiosis with nitrogen-fixing microbes, are attractive future options that nevertheless require more intensive and internationally coordinated research efforts. Although nitrogen-fixing plants may be less productive, at some point agriculture must significantly reduce the use of warming (chemically synthesized) N and give priority to the biological nitrogen fixation, if it is to sustain both food production and environmental health for a continuously growing human population.

Concepts: Agriculture, Ammonia, Fertilizer, Nitrogen, Nitrogen fixation, Denitrification, Nitrification, Nitrogen cycle