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Biogeochemical dynamics underlying equilibrium between nitrogen fixation and denitrification and its impact on a coastal marine ecosystem model
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A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential
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Computational and Experimental Study for the Denitrification of Biomass-Derived Hydrothermal Liquefaction Oil
Hydrothermal liquefaction (HTL) is a promising method for processing wet biomass and waste feedstock to produce biofuels. During the HTL process, proteins and other biomolecules in certain feedstock get converted into nitrogenous compounds in produced biocrude, which represents a major challenge to further upgrading them into fuels. One promising approach is to separate nitrogenous compounds from the biocrude using polymeric resins. In this study, experiments were conducted to down-select sorbent and resin systems using a nitrogen-compound-containing surrogate biocrude. We model the binding interactions between an Amberlyst polymeric resin with various compounds present in the biocrude mixture such as nitrogenous compounds like pyrrole, pyridine, hexanamide, and representative co-existing compounds like phenol and dodecanoic acid. To ascertain the efficiency of various resins in the denitrogenation process, we have developed a quantitative structure–function model for the interacting components in the mixture. Our results suggest that the Amberlyst resin is a viable candidate for efficient removal of target nitrogen-containing compounds (such as pyridine) from the biocrude as a result of favorable interactions. The computational studies provide some insight into how and why the identified resin (Amberlyst) works in selective extraction of nitrogenous compound(s).
The influence of tillage and fertilizer on the flux and source of nitrous oxide with reference to atmospheric variation using laser spectroscopy
Nitrous oxide (N 2 O) is the third most important long-lived greenhouse gas and agriculture is the largest source of N 2 O emissions. Curbing N 2 O emissions requires understanding influences on the flux and sources of N 2 O. We measured flux and evaluated microbial sources of N 2 O using site preference ( S P ; the intramolecular distribution of 15 N in N 2 O) in flux chambers from a grassland tilling and agricultural fertilization experiments and atmosphere. We identified values greater than that of the average atmosphere to reflect nitrification and/or fungal denitrification and those lower than atmosphere as increased denitrification. Our spectroscopic approach was based on an extensive calibration with 18 standards that yielded S P accuracy and reproducibility of 0.7 ‰ and 1.0 ‰, respectively, without preconcentration. Chamber samples from the tilling experiment taken ~ monthly over a year showed a wide range in N 2 O flux (0–1.9 g N 2 O-N ha -1 d -1 ) and S P (- 1.8 to 25.1 ‰). Flux and S P were not influenced by tilling but responded to sampling date. Large fluxes occurred in October and May in no-till when soils were warm and moist and during a spring thaw, an event likely representing release of N 2 O accumulated under snow cover. These high fluxes could not be ascribed to a single microbial process as S P differed among chambers. However, the year-long S P and flux data for no-till showed a slight direct relationship suggesting that nitrification increased with flux. The comparative data in till showed an inverse relationship indicating that high flux events are driven by denitrification. Corn ( Zea mays ) showed high fluxes and S P values indicative of nitrification ~ 4 wk after fertilization with subsequent declines in S P indicating denitrification. Although there was no effect of fertilizer treatment on flux or S P in switchgrass ( Panicum virgatum) , high fluxes occurred ~1 month after fertilization. In both treatments, S P was indicative of denitrification in many instances, but evidence of nitrification/fungal denitrification also prevailed. At 2 m atmospheric N 2 O S P had a range of 31.1 ‰ and 14.6 ‰ in the grassland tilling and agricultural fertilization experiments, respectively. These data suggest the influence of soil microbial processes on atmospheric N 2 O and argue against the use of the global average atmospheric S P in isotopic modeling approaches.
Emergence and disruption of cooperativity in a denitrifying microbial community
Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N 2 O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N 2 O. Microbial denitrification is a primary contributor to biotic production of N 2 O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO 3 − ) contaminated superfund site, complete denitrification through the exchange of nitrite (NO 2 − ) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO 3 − , cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO 2 − , which disrupts denitrification causing N 2 O off gassing.
Glacial‐Interglacial and Millennial‐Scale Changes in Nitrous Oxide Emissions Pathways and Source Regions
During the transition from the Last Glacial Maximum (LGM) to the Holocene, the atmospheric N 2 O mole fraction increased by 80 nmol mol −1 . Using ice core measurements of N 2 O isotopomer ratios, we show that this increase was driven by increases in both nitrification and denitrification, with the relative partitioning between both production pathways depending on the assumed isotopic end-member source signatures. Similarly, we also attribute a 35 nmol mol −1 N 2 O mole fraction increase during the Heinrich Stadial 4/Dansgaard Oeschger 8 (HS4/DO8) millennial-scale event to increases in both N 2 O production pathways. In contrast, the 25 nmol mol −1 N 2 O mole fraction decrease during the Younger Dryas was driven almost exclusively by a decrease in nitrification. The deglacial and HS4/DO8 increases in N 2 O production occurred in both marine and terrestrial environments, with the terrestrial source responding faster to warming by about two centuries. Constraints on changes in nitrification and denitrification emissions are robust and consistent with previous studies showing the sensitivity of N 2 O emissions to abrupt Northern Hemisphere warming. This study demonstrates for the first time the importance of both denitrification and nitrification pathways in driving source changes. Absolute emissions are more uncertain due to uncertainty about source isotopomer signatures. For instance, the contribution of denitrification to emissions at the LGM shifts from (65 ± 10) % to (91 ± 6) % when factoring in isotope enrichment due to partial reduction of N 2 O to N 2 during denitrification. Reducing uncertainty in source signatures will increase the power of ice core N 2 O isotope records in deducing environmental change.
Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) (Final Scientific/Technical Report, Subcontract Award No. 6953691)
The overarching objective the Baliga lab is to develop a mechanistic understanding of the field relevant metabolic processes underlying community partitioning of respiration pathways and physiological state shifts. In order to dissect how environmental perturbations influence microbial regulatory networks, we have constructed data-driven models that capture the dynamic interplay between abiotic and biotic factors during laboratory simulations. Specifically, we have developed multiple computational models (i.e., cMonkey2, EGRIN 2.0, and multiple genome-scale metabolic models) connecting environmental influence to genome-encoded regulatory programs. In addition, we have generated new tools such as Live Anaerobic Cell Sorting (LAnCS) and Fluidized Bed Reactors (FBRs) to investigate the dynamics of community partitioning of metabolic processes supporting sulfate or nitrate respiration, which are two critical activities observed from the field site at Oak Ridge National Labs (ORNL). This framework of connecting field phenomena with laboratory simulations and computational modeling has created the Environmental Simulations and Modelling (EnvSim) campaign within ENIGMA. The campaign, which spans multiple laboratories across ENIGMA and is led by the Baliga group, has established synthetic communities (SynComs) to discover, characterize, and dissect key microbial processes relevant to field observations, such as emissions of the greenhouse gas nitrous oxide (N 2 O). For example, the EnvSim campaign so far has deduced four potential mechanisms that may account for the N 2 O emissions at the FRC and are currently being investigated by labs across ENIGMA. Denitrification may be driven by complete denitrifiers, however, their NosZ enzymes, which catalyze the final step in denitrification by converting N 2 O to N 2 , may be sensitive at a lower pH. Additionally, the denitrification process could be partitioned among organisms and some may have pH-sensitive NosZ genes. Another factor contributing to variable N 2 O emissions relates to the metal co-factors involved in the denitrification pathway. For instance, excess Cu, Al, Mn, U, Ni, Co, Cu, and/or Cd may have inhibitory effects on multiple enzymatic steps during denitrification, while the enzymatic production of nitrite, the precursor of N 2 O, can be limited by the essential metal Mo. Lastly, abiotic production of N 2 O may occur as a result of chemodenitrification, in which metals like Fe, Mn, and some organic compounds can drive redox reactions that convert nitrogen cycle intermediates to N 2 O under the right conditions. Current investigations and analyses have generated multiple transcriptomic profiles aiding the refinement of new metabolic and gene regulatory network model for our denitrifying SynCom. In sum, the previous funding cycle has generated 33 peer-reviewed publications spanning predictive network biology to co-operativity of mutualistic interspecies interactions of evolved communities. Our integration of multiple omics datasets and the development of new network modelling tools has revealed important insights that can explain field observed phenomenon and generated new hypotheses to be investigated in the field.
Tuning Local Atomic Structures in MoS 2 Based Catalysts for Electrochemical Nitrate Reduction
In recent years, there has been a substantial surge in the investigation of transition-metal dichalcogenides such as MoS 2 as a promising electrochemical catalyst. Inspired by denitrification enzymes such as nitrate reductase and nitrite reductase, the electrochemical nitrate reduction catalyzed by MoS 2 with varying local atomic structures is reported. Further, it is demonstrated that the hydrothermally synthesized MoS 2 containing sulfur vacancies behaves as promising catalysts for electrochemical denitrification. With copper doping at less than 9% atomic ratio, the selectivity of denitrification to dinitrogen in the products can be effectively improved. X-ray absorption characterizations suggest that two sulfur vacancies are associated with one copper dopant in the MoS 2 skeleton. DFT calculation confirms that copper dopants replace three adjacent Mo atoms to form a trigonal defect-enriched region, introducing an exposed Mo reaction center that coordinates with Cu atom to increase N 2 selectivity. Apart from the higher activity and selectivity, the Cu-doped MoS 2 also demonstrates remarkably improved tolerance toward oxygen poisoning at high oxygen concentration. Finally, Cu-doped MoS 2 based catalysts exhibit very low specific energy consumption during the electrochemical denitrification process, paving the way for potential scale-up operations.
Copper availability governs nitrous oxide accumulation in wetland soils and stream sediments
Denitrification is microbially-mediated through enzymes containing metal cofactors. Laboratory studies of pure cultures have highlighted that the availability of Cu, required for the multicopper enzyme nitrous oxide reductase, can limit N2O reduction. However, in natural aquatic systems, such as wetlands and hyporheic zones in stream beds, the role of Cu in controlling denitrification remains incompletely understood. In this study, we collected soils and sediments from three natural environments -- riparian wetlands, marsh wetlands, and a stream -- to investigate their nitrogen species transformation activity at background Cu levels and different supplemented Cu loadings. All of the systems contained solid-phase associated Cu below or around geological levels (40 - 280 nmol g-1) and exhibited low dissolved Cu (3-50 nM), which made them appropriate sites for evaluating the effect of limited Cu availability on denitrification. In laboratory incubation experiments, high concentrations of N2O accumulated in all microcosms lacking Cu amendment except for one stream sediment sample. With Cu added to provide dissolved concentrations at trace levels (10-300 nM), reduction rate of N2O to N 2 in the wetland soils and stream sediments was enhanced. A kinetic model could account for the trends in nitrogen species by combining the reactions for microbial reduction of NO 3 - to NO 2 -/N 2 O/N 2 and abiotic reduction of NO 2 - to N 2 . The model revealed that the rate of N 2 O to N 2 conversion increased significantly in the presence of Cu. For riparian wetland soils and stream sediments, the kinetic model also suggested that overall denitrification is driven by abiotic reduction of NO2- in the presence of inorganic electron donors. This study demonstrated that natural aquatic systems containing Cu at concentrations less than or equal to crustal abundances may display incomplete reduction of N 2 O to N 2 that would cause N 2 O accumulation and release to the atmosphere.
Influence of Agricultural Managed Aquifer Recharge (AgMAR) and Stratigraphic Heterogeneities on Nitrate Reduction in the Deep Subsurface
Agricultural managed aquifer recharge (AgMAR) is a strategy whereby surface water is used to intentionally flood croplands to recharge underlying aquifers. However, nitrate (NO 3 - ) contamination in agriculturally intensive regions poses a threat to groundwater resources under AgMAR. We use a reactive transport model to understand the effects of AgMAR management strategies (i.e., by varying the frequency, duration between flooding events, and amount of water) on NO 3 - leaching to groundwater under different stratigraphic configurations and antecedent moisture conditions. We examine the potential of denitrification and nitrogen retention in deep vadose zone sediments (~15 m) using variable AgMAR application rates on two-dimensional representations of differently textured soils, soils with discontinuous bands/channels, and with preferential flow paths characteristic of agricultural fields. Simulations indicate finer textured sediments, alone or embedded within/adjacent to high flow regions, are important reducing zones providing conditions needed for denitrification. Simulation results suggest that applying water all-at-once rather than in increments transports higher concentrations of NO 3 - deeper into the profile, which may exacerbate groundwater quality. This transport into deeper depths can be aggravated by wetter antecedent soil moisture conditions. However, applying water all-at-once also increases denitrification within the vadose zone by promoting anoxic conditions. We conclude that AgMAR can be designed to enhance denitrification in the subsurface and reduce NO 3 - leaching to groundwater, while specifically accounting for lithologic heterogeneity, antecedent soil moisture conditions, and depth to the water table. Our findings are potentially relevant to other systems that experience flooding inundation such as floodplains and dedicated recharge basins.
Scaling hyporheic nitrogen cycling in large river alluvial aquifers
Research Element 1: Denitrification is a difficult flux to measure when fluxes are low and when the ecosystem is difficult to sample. These attributes describe Nyack floodplain, a large gravel-bedded aquifer adjacent to the Middle Fork Flathead River. Given that denitrification is simply respiration with nitrate as a terminal electron acceptor, we reasoned that N 2 production should negatively covary with oxygen respiration so long that oxygen is available. We sampled 16 wells 8 times throughout a year and analyzed these water samples on a membrane-inlet mass spectrometer for N 2 :Ar and O 2 . We fit multilevel models to N 2 :Ar as a function of dissolved oxygen. Within wells, there was no relationship between O 2 and N 2 :Ar. Among wells N 2 :Ar increased as O 2 declined. Based on the slope of this relationship, ~ -0.07, and estimated oxygen respiration in Nyack derived from prior studies, a possible range for denitrification is 0-8 mmol m -2 d -1 corresponding to a turnover rate for nitrate of 0-0.2/d. This estimated turnover rate is in the lower 20% of rates measured in the LINX 2 study, yet shows that even in a low nitrate (0.005 mmol/L) aquifer denitrification can be a substantial sink for dissolved N. Research Element 3 and 4: We developed a new theoretical approach to describe the relationship between water inflow, water outflow, and water age in porous media control volumes under dynamic flow conditions. Our approach had three distinct steps. First we described the application of well-established equations borrowed from Chemical Engineering to describe water age distributions in the hyporheic zone under steady state conditions. We published the associated results in the scientific journal PLOS ONE. Second, we developed a new theory ("flow spans") to describe how predicted steady-state water age distributions will respond to time varying imbalances in hyporheic discharge and recharge. Finally, we developed a proof-of-concept simulation model based on the new theory and used the model to examine the effects of flow regulation on a simulated river with characteristics representative of western U.S. montane rivers with expansive hyporheic zones.