Restoration impacts on rates of denitrification and greenhouse gas fluxes from tropical coastal wetlands

Forested coastal wetlands are globally important systems sequestering carbon and intercepting nitrogen pollution from nutrient-rich river systems. Coastal wetlands that have suffered extensive disturbance are the target of comprehensive restoration efforts. Accurate assessment of restoration success requires detailed mechanistic understanding of wetland soil biogeochemical functioning across restoration chrono-sequences, which remains poorly understood for these sparsely investigated systems. This study investigated denitrification and greenhouse gas fluxes in mangrove and Melaleuca forest soils of Vietnam, using the ¹⁵N-Gas flux method. Denitrification-derived N₂O was significantly higher from Melaleuca than mangrove forest soils, despite higher potential rates of total denitrification in the mangrove forest soils (8.1 ng N g^-1 h^-1) than the Melaleuca soils (6.8 ng N g^-1 h^-1). Potential N₂O and CO₂ emissions were significantly higher from the Melaleuca soils than from the mangrove soils. Disturbance and subsequent recovery had no significant effect on N biogeochemistry except with respect to the denitrification product ratio in the mangrove sites, which was highest from the youngest mangrove site. Potential CO₂ and CH₄ fluxes were significantly affected by restoration in the mangrove soils. The lowest potential CO₂ emissions were observed in the mid-age plantation and potential CH₄ fluxes decreased in the older forests. The mangrove system, therefore, may remove excess N and improve water quality with low greenhouse gas emissions, whereas in Melaleucas, increased N₂O and CO₂ emissions also occur. These emissions are likely balanced by higher carbon stocks observed in the Melaleuca soils. These mechanistic insights highlight the importance of ecosystem restoration for pollution attenuation and reduction of greenhouse gas emissions from coastal wetlands. Restoration efforts should continue to focus on increasing wetland area and function, which will benefit local communities with improved water quality and potential for income generation under future carbon trading.

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.

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil

Nitrate (NO₃^-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO₃^- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g^-1 h^-1and 2.4125-58.682 nmol N g^-1 h^-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO₃^- reduction, hence dominated NO₃^- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO₃^- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.

Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.

Nitrogen and carbon concentrations and stable isotope ratios: Data from a 15N tracer study in short-form Spartina alterniflora and Distichlis spicata

We present four datasets that provide information on primary production, nitrogen (N) uptake and allocation in two salt marsh grasses, short-form Spartina alterniflora and Distichlis spicata. These four datasets were generated during a month-long stable isotope (15N) tracer study described in the companion manuscript (Hill et al., 2018). They include an allometry dataset containing mass and height data for individual plants harvested from Colt State Park, Bristol, Rhode Island and used to nondestructively estimate plant masses. A second dataset contains weekly stem height measurements collected over the course of the 15N tracer study. Also included are high resolution data from 49 vegetated compartments (leaves, stems, fine/coarse roots, rhizomes) and bulk sediment depth intervals, reporting the mass, carbon and N concentrations, and stable isotope ratios measured following the harvest of cores over time. Additionally, we provide a complementary dataset with estimates of microbial removal from potential and ambient denitrification enzyme assays. These data, along with source code used in their analysis, are compiled in the NitrogenUptake2016 R package available from the Comprehensive R Archive Network.

Denitrification Capacity of a Natural and a Restored Marsh in the Northern Gulf of Mexico

Anthropogenic pressures, such as diking, construction of dams, and oil spills negatively impact coastal marshes creating growing pressure to preserve and to restore salt marshes due to their critical role in permanently removing nitrate runoff through denitrification as well as other ecosystem services they provide. This study determined denitrification rates across a typical northern Gulf of Mexico salt marsh landscape that included a natural marsh, a tidal creek, and a 21-year-old restored salt marsh. Denitrification capacity, measured with the isotope pairing technique on a membrane inlet mass spectrometer, was comparable across the sites despite significant differences in above and below ground characteristics. Total extractable ammonium concentrations and sediment carbon content were higher at the natural marsh compared to the restored marsh. Hydrogen sulfide concentrations were highest at the creek compared to the vegetated sites and lowest at the restored marsh. This suggests that marsh restoration projects reestablish nitrogen removal capacity at rates similar to those in natural systems and can help to significantly reduce nitrogen loads to the coastal ocean.

Nitrogen uptake and allocation estimates for Spartina alterniflora and Distichlis spicata

Salt marshes have the potential to intercept nitrogen that could otherwise impact coastal water quality. Salt marsh plants play a central role in nutrient interception by retaining N in above- and belowground tissues. We examine N uptake and allocation in two dominant salt marsh plants, short-form Spartina alterniflora and Distichlis spicata. Nitrogen uptake was measured using ¹⁵N tracer experiments conducted over a four-week period, supplemented with stem-level growth rates, primary production, and microbial denitrification assays. By varying experiment duration, we identify the importance of a rarely-measured aspect of experimental design in ¹⁵N tracer studies. Experiment duration had a greater impact on quantitative N uptake estimates than primary production or stem-level relative growth rates. Rapid initial scavenging of added ¹⁵N caused apparent nitrogen uptake rates to decline by a factor of two as experiment duration increased from one week to one month, although each experiment shared the qualitative conclusion that Distichlis roots scavenged N approximately twice as rapidly as Spartina. We estimate total N uptake into above- and belowground tissues as 154 and 277 mg N·m^-2·d^-1 for Spartina and Distichlis, respectively. Driving this pattern were higher N content in Distichlis leaves and belowground tissue and strong differences in primary production; Spartina and Distichlis produced 8.8 and 14.7 g biomass·m^-2·d^-1. Denitrification potentials were similar in sediment associated with both species, but the strong species-specific difference in N uptake suggests that Distichlis-dominated marshes are likely to intercept more N from coastal waters than are short-form Spartina marshes. The data and source code for this manuscript are available as an R package from https://github.com/troyhill/NitrogenUptake2016.

A meta-analysis of soil salinization effects on nitrogen pools, cycles and fluxes in coastal ecosystems

Salinity intrusion caused by land subsidence resulting from increasing groundwater abstraction, decreasing river sediment loads and increasing sea level because of climate change has caused widespread soil salinization in coastal ecosystems. Soil salinization may greatly alter nitrogen (N) cycling in coastal ecosystems. However, a comprehensive understanding of the effects of soil salinization on ecosystem N pools, cycling processes and fluxes is not available for coastal ecosystems. Therefore, we compiled data from 551 observations from 21 peer-reviewed papers and conducted a meta-analysis of experimental soil salinization effects on 19 variables related to N pools, cycling processes and fluxes in coastal ecosystems. Our results showed that the effects of soil salinization varied across different ecosystem types and salinity levels. Soil salinization increased plant N content (18%), soil NH₄⁺ (12%) and soil total N (210%), although it decreased soil NO₃^- (2%) and soil microbial biomass N (74%). Increasing soil salinity stimulated soil N₂ O fluxes as well as hydrological NH₄⁺ and NO₂^- fluxes more than threefold, although it decreased the hydrological dissolved organic nitrogen (DON) flux (59%). Soil salinization also increased the net N mineralization by 70%, although salinization effects were not observed on the net nitrification, denitrification and dissimilatory nitrate reduction to ammonium in this meta-analysis. Overall, this meta-analysis improves our understanding of the responses of ecosystem N cycling to soil salinization, identifies knowledge gaps and highlights the urgent need for studies on the effects of soil salinization on coastal agro-ecosystem and microbial N immobilization. Additional increases in knowledge are critical for designing sustainable adaptation measures to the predicted intrusion of salinity intrusion so that the productivity of coastal agro-ecosystems can be maintained or improved and the N losses and pollution of the natural environment can be minimized.

Gross nitrous oxide production drives net nitrous oxide fluxes across a salt marsh landscape

Sea level rise will change inundation regimes in salt marshes, altering redox dynamics that control nitrification - a potential source of the potent greenhouse gas, nitrous oxide (N2 O) - and denitrification, a major nitrogen (N) loss pathway in coastal ecosystems and both a source and sink of N2 O. Measurements of net N2 O fluxes alone yield little insight into the different effects of redox conditions on N2 O production and consumption. We used in situ measurements of gross N2 O fluxes across a salt marsh elevation gradient to determine how soil N2 O emissions in coastal ecosystems may respond to future sea level rise. Soil redox declined as marsh elevation decreased, with lower soil nitrate and higher ferrous iron in the low marsh compared to the mid and high marshes (P < 0.001 for both). In addition, soil oxygen concentrations were lower in the low and mid-marshes relative to the high marsh (P < 0.001). Net N2 O fluxes differed significantly among marsh zones (P = 0.009), averaging 9.8 ± 5.4 μg N m(-2)  h(-1) , -2.2 ± 0.9 μg N m(-2)  h(-1) , and 0.67 ± 0.57 μg N m(-2)  h(-1) in the low, mid, and high marshes, respectively. Both net N2 O release and uptake were observed in the low and high marshes, but the mid-marsh was consistently a net N2 O sink. Gross N2 O production was highest in the low marsh and lowest in the mid-marsh (P = 0.02), whereas gross N2 O consumption did not differ among marsh zones. Thus, variability in gross N2 O production rates drove the differences in net N2 O flux among marsh zones. Our results suggest that future studies should focus on elucidating controls on the processes producing, rather than consuming, N2 O in salt marshes to improve our predictions of changes in net N2 O fluxes caused by future sea level rise.