Understanding the hydrologic control of N cycle: Effect of water filled pore space on heterotrophic nitrification, denitrification and dissimilatory nitrate reduction to ammonium mechanisms in unsaturated soils

Isotopomeric Peak Assignment for N2O in Cross-Labeling Experiments by Fiber-Enhanced Raman Multigas Spectroscopy

Human intervention in nature, especially fertilization, greatly increased the amount of N2O emission. While nitrogen fertilizer is used to improve nitrogen availability and thus plant growth, one negative side effect is the increased emission of N2O. Successful regulation and optimization strategies require detailed knowledge of the processes producing N2O in soil. Nitrification and denitrification, the main processes responsible for N2O emissions, can be differentiated using isotopic analysis of N2O. The interplay between these processes is complex, and studies to unravel the different contributions require isotopic cross-labeling and analytical techniques that enable tracking of the labeled compounds. Fiber-enhanced Raman spectroscopy (FERS) was exploited for sensitive quantification of N2O isotopomers alongside N2, O2, and CO2 in multigas compositions and in cross-labeling experiments. FERS enabled the selective and sensitive detection of specific molecular vibrations that could be assigned to various isotopomer peaks. The isotopomers 14N15N16O (2177 cm-1) and 15N14N16O (2202 cm-1) could be clearly distinguished, allowing site-specific measurements. Also, isotopomers containing different oxygen isotopes, such as 14N14N17O, 14N14N18O, 15N15N16O, and 15N14N18O could be identified. A cross-labeling showed the capability of FERS to disentangle the contributions of nitrification and denitrification to the total N2O fluxes while quantifying the total sample headspace composition. Overall, the presented results indicate the potential of FERS for isotopic studies of N2O, which could provide a deeper understanding of the different pathways of the nitrogen cycle.

Labile carbon and soil texture control nitrogen transformation in deep vadose zone

Understanding transient nitrogen (N) storage and transformation in the deep vadose zone is critical for controlling groundwater contamination by nitrate. The occurrence of organic and inorganic forms of carbon (C) and nitrogen and their importance in the deep vadose zone is not well characterized due to difficulty in sampling and the limited number of studies. We sampled and characterized these pools beneath 27 croplands with different vadose zone thicknesses (6-45 m). We measured nitrate and ammonium in different depths for the 27 sites to evaluate inorganic N storage. We measured total Kjeldahl nitrogen (TKN), hot-water extractable organic carbon (EOC), soil organic carbon (SOC), and δ¹³C for two sites to understand the potential role of organic N and C pools in N transformations. Inorganic N stocks in the vadose zone were 21.7-1043.6 g m^-2 across 27 sites; the thicker vadose zone significantly stored more inorganic N (p < 0.05). We observed significant reservoirs of TKN and SOC at depths, likely representing paleosols that may provide organic C and N to subsurface microbes. The occurrence of deep C and N needs to be addressed in future research on terrestrial C and N storage potential. The increase of ammonium and EOC and δ¹³C value in the proximity of these horizons is consistent with N mineralization. An increase of nitrate, concurrent with the sandy soil texture and the water-filled pore space (WFPS) of 78 %, suggests that deep vadose zone nitrification may be supported in vadose zones with organic-rich layers such as paleosol. A profile showing the decrease of nitrate concentrations, concurrent with the clay soil texture and the WFPS of 91 %, also suggests denitrification may be an important process. Our study shows that microbial N transformation may be possible even in deep vadose zone with co-occurrence of C and N sources and controlled by labile C availability and soil texture.

Matrix-associated microbial communities in a nitrogen-removing on-site wastewater treatment system are largely structured by niche processes

On-site wastewater treatment systems (OWTSs) can be designed to promote microbial communities with naturally occurring metabolic functions desirable to wastewater treatment. Among such OWTSs are nitrogen-removing biofilters (NRBs), comprising a sand layer overlying a sand-lignocellulose (sand-lc) layer and intended to promote sequential nitrification and denitrification. The design of NRBs is based on the hypothesis that niche processes like environmental selection strongly structure the microbial communities, which predicts that immigrating wastewater communities and matrix-associated communities will be distinct and that the matrix communities in the two layers will be distinct. We characterized NRB microbial communities by 16S ribosomal RNA amplicon sequencing. Selection of the matrix-associated communities was indicated by clear differences from the immigrating community. For matrix-associated communities, alpha and beta diversity differed between the matrix layers, as did the relative abundances of many functional groups and genera. Functional groups with strict metabolisms were nearly exclusively detected in either the sand (ammonia and nitrite oxidizers) or sand-lc layer (methanogens), consistent with the niche hypothesis. Contrary to expectations, denitrifiers as a functional group were not present at greater relative abundance in the sand-lc than sand matrix because of a portfolio effect: some denitrifying genera were more abundant in the sand layer, whereas others were more abundant in the sand-lc layer. This study reveals niche processes acting at different levels of community organization for different biogeochemical functions, a crucial consideration in designing effective and reliable OWTSs to mitigate nitrogen pollution.

Effects of different drainage conditions on nitrogen losses of an agricultural sandy loam soil

Prolonged waterlogging in agricultural fields has severe consequences for the crop development and growth, and could potentially lead to higher N losses. In this study, a 3.93 ha agricultural field in Denmark was separated into two parts of well-drained (WD) and poorly-drained (PD) based on the installation depth of the tile drains. The field was continuously monitored for drainage, soil water dynamics, nitrogen leaching through the drains, and grain dry matter and nitrogen yields in a 4-year period (2017-2020). Furthermore, denitrification potential of the top 1 m of the soil at both parts of the field was measured through the denitrifying enzyme activity assay, and a 1D Daisy model was utilized to capture the differences between water and nitrogen balances at WD and PD. Results indicated that on average over the 4 years, annual harvested nitrogen in the crops at PD was 14% lower compared to WD, with a significant reduction of 33% in 2017-2018, that coincided with the longest period of waterlogging at PD. Moreover, greater losses of nitrogen through leaching from drainage and other pathways were measured at the PD (109 kg N ha^-1 ya^-1) compared to the WD (95 kg N ha^-1 ya^-1). Based on the simulations, losses through preferential flow pathways to the drains dominated at PD and most of the denitrification is expected to occur within the topsoil. Future studies could significantly benefit from monitoring the redox dynamics in the top 30 cm of the PD soils, and increasing the depth of tiles drains by redrainage could reduce the N losses of poorly drained agricultural soils.

Reactive Transport of NH4+ in the Hyporheic Zone from the Ground Water to the Surface Water

Nowadays, ammonia nitrogen (NH4+) pollution gets more and more attention in drinking water sources. This study investigated the main behavior of biogeochemical NH4+ from groundwater to surface water in a hyporheic zone (HZ) sediment from a reservoir. The experiments were conducted using synthetic groundwater to investigate ammonium transformation. The results indicated that ammonium concentration decreased, apparently resulting from the influence of microbial oxidation and ion exchange with Ca2+, Mg2+, K+, and Na+. However, all the ammonium in the sediment was oxidized, then the adsorbed NH4+ became bioavailable by being released back when NH4+ concentration decreased in the aqueous phase. The results showed NH4+ behavior in a HZ where the aerobic and anaerobic environments frequently exchange, with different hydrological conditions controlled by a strong coupling between microbial activities, geochemistry, hydrology, and ion exchange.

Aromatic compounds releases aroused by sediment resuspension alter nitrate transformation rates and pathways during aerobic-anoxic transition

Aromatic compounds (ACs) releases aroused by sediment resuspension would certainly change the concentrations of suspended sediment (SPS) and organic carbon, which may alter nitrate-N transformation during aerobic-anoxic transition. To prove this, three typical ACs (aniline, nitrobenzene, and methylbenzene) with different octanol-water partition coefficients (K_ow) were selected to investigate the effects of ACs releases aroused by sediment resuspension on nitrate-N transformation during aerobic-anoxic transition. ACs releases aroused by sediment resuspension accelerated nitrate-N transformation and enhanced the potential for dissimilatory nitrate reduction to ammonium (DNRA), compared to that without sediment resuspension. With sediment resuspension, methylbenzene releases affected nitrate-N transformation rates and pathways more significantly than aniline and nitrobenzene releases. Microbial analysis indicated that sediment resuspension created complicated microbial co-occurrence networks and changed the associations among bacteria; dominant bacteria abundance varied with different ACs releases. Further analysis revealed that ACs distributed in SPS, which increased with logK_ow, indirectly affected nitrate-N transformation rates and pathways via altering dominant bacteria abundance and electron transport system activity (ETSA). Especially, ETSA, which was positively associated with ACs distributed in SPS, affected nitrate-N transformation most directly. Overall, ACs release fate played important roles in nitrate-N transformation, causing ammonia-N retention and alterations in nitrogen cycle during aerobic-anoxic transition.

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO₃^- occurs in two steps; in the first step, NO₃^- is reduced to NO₂^-; and in the second, unlike denitrification, NO₂^- is reduced to NH₄⁺ without intermediates. There are two sets of NO₃^-/NO₂^- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N₂O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N₂O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO₂^-/NO₃^- ratio, and concentrations of ferrous iron (Fe²⁺) and sulfide (S^2-). Under low-redox conditions, a high C/NO₃^- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO₃^- are equal, the NO₂^-/NO₃^- ratio modulates partitioning of NO₃^-, and a high NO₂^-/NO₃^- ratio favours DNRA. A high S^2-/NO₃^- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO₃^- to NH₄⁺, it is essential for protecting NO₃^- from leaching and gaseous (N₂O) losses and enriches soils with readily available NH₄⁺-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO₃^- pollution, enhance soil health and improve environmental quality.

NH4+-N/NO3--N ratio controlling nitrogen transformation accompanied with NO2--N accumulation in the oxic-anoxic transition zone

Although nitrogen (N) transformations have been widely studied under oxic or anoxic condition, few studies have been carried out to analyze the transformation accompanied with NO₂^--N accumulation. Particularly, the control of mixed N species in N-transformation remains unclear in an oxic-anoxic transition zone (OATZ), a unique and ubiquitous redox environment. To bridge the gap, in this study, OATZ microcosms were simulated by surface water and sediments of a shallow lake. The N-transformation processes and rates at different NH₄⁺-N/NO₃^--N ratios, and NO₂^--N accumulations in these processes were evaluated. N-transformation process exhibited a turning point. Simultaneous nitrification and denitrification occurred in its early stage (first 10 days, dissolved oxygen (DO) ≥ 2 mg/L) and then denitrification dominated (after 10 days, DO < 2 mg/L), which were not greatly affected by the NH₄⁺-N/NO₃^--N ratio, on the contrary, the transformation rates of NH₄⁺-N and NO₃^--N were distinctly affected. The NH₄⁺-N transformation rates were positively correlated with the NH₄⁺-N/NO₃^--N ratio. The highest NO₃^--N transformation rate was observed at an NH₄⁺-N/NO₃^--N ratio of 1:1 with organic carbon/NO₃^--N of 3.09. The NO₂^--N accumulation, which increased with the decrease in NH₄⁺-N/NO₃^--N ratio, was also controlled by organic carbon concentration and type. The peak concentration of NO₂^--N accumulation occurred only when the NO₃^--N transformation rate was particularly low. Thus, NO₂^--N accumulation may be reduced by adjusting the control parameters related to N and organic carbon sources, which enhances the theoretical insights for N-polluted aquatic ecosystem bioremediation.

Co-transport behavior of ammonium and colloids in saturated porous media under different hydrochemical conditions

To investigate co-transport behavior of ammonium and colloids in saturated porous media under different hydrochemical conditions, NH₄⁺ was selected as the target contaminant, and silicon and humic acid (HA) were selected as typical organic and inorganic colloids in groundwater. Column experiments were then conducted to investigate the transport of NH₄⁺ colloids under various hydrochemical conditions. The results showed that because of the different properties of colloidal silicon and HA after combining with NH₄⁺, the co-transport mechanism became significantly different. During transport by the NH₄⁺-colloid system, colloidal silicon occupied the adsorption sites on the medium surface to promote the transport of NH₄⁺, while humic acid (HA) increased the number of adsorption sites of the medium to hinder the transport of NH₄⁺. The co-transport of NH₄⁺ and colloids is closely related to hydrochemical conditions. In the presence of HA, competitive adsorption and morphological changes of HA caused NH₄⁺ to be more likely to be transported at a higher ionic strength (IS = 0.05 m, CaCl₂) and alkalinity (pH = 9.3). In the presence of colloidal silicon, blocking action caused the facilitated transport to be dependent on higher ionic strength and acidity (pH = 4.5), causing the recovery of NH₄⁺ to improve by 7.99%, 222.25% (stage 1), and 8.63%, respectively. Moreover, transport increases with the colloidal silicon concentrations of 20 mg/L then declines at 40 mg/L, demonstrating that increased concentrations will lead to blocking and particle aggregation, resulting in delayed release in the leaching stage. Graphical abstract.

In-situ study of migration and transformation of nitrogen in groundwater based on continuous observations at a contaminated desert site

The objective of this study was to explore the controlling factors on the migration and transformation of nitrogenous wastes in groundwater using long-term observations from a contaminated site on the southwestern edge of the Tengger Desert in northwestern China. Contamination was caused by wastewater discharge rich in ammonia. Two long-term groundwater monitoring wells (Wells 1# and 2#) were constructed, and 24 water samples were collected. Five key indicators were tested: ammonia, nitrate, nitrite, dissolved oxygen, and manganese. A numerical method was used to simulate the migration process and to determine the migration stage of the main pollutant plume in groundwater. The results showed that at Well 1# the nitrogenous waste migration process had essentially been completed, while at Well 2# ammonia levels were still rising and gradually transitioning to a stable stage. The differences for Well 1# and Well 2# were primarily caused by differences in groundwater flow. The change in ammonia concentration was mainly controlled by the migration of the pollution plume under nitrification in groundwater. The nitrification rate was likely affected by changes in dissolved oxygen and potentially manganese.