Microscale pH variations during drying of soils and desert biocrusts affect HONO and NH3 emissions

Ammonia emissions from a dairy housing and wastewater treatment plant quantified with an inverse dispersion method accounting for deposition loss

Ammonia (NH3) emissions negatively impact air, soil, and water quality, hence human health and biodiversity. Significant emissions, including the largest sources, originate from single or multiple structures, such as livestock facilities and wastewater treatment plants (WWTPs). The inverse dispersion method (IDM) is effective in measuring total emissions from such sources, although depositional loss between the source and point of measurement is often not accounted for. We applied IDM with a deposition correction to determine total emissions from a representative dairy housing and WWTP during several months in autumn and winter in Switzerland. Total emissions were 1.19 ± 0.48 and 2.27 ± 1.53 kg NH3 d-1 for the dairy housing and WWTP, respectively, which compared well with literature values, despite the paucity of WWTP data. A concurrent comparison with an inhouse tracer ratio method at the dairy housing indicated an offset of the IDM emissions by < 20%. Diurnal emission patterns were evident at both sites mostly driven by changes in air temperature with potential lag effects such as following sludge agitation. Modeled deposition corrections to adjust the concentration loss detected at the measurement point with the associated footprint were 22-28% of the total emissions and the cumulative fraction of deposition to emission modeled with distance from the source was between 7% and 12% for the measurement distances (60-150 m). Although estimates of depositional loss were plausible, the approach is still connected with substantial uncertainty, which calls for future validation measurements. Longer measurement periods encompassing more management activities and environmental conditions are required to assess predictor variable importance on emission dynamics. Combined, IDM with deposition correction will allow the determination of emission factors at reduced efforts and costs, thereby supporting the development and assessment of emission reducing methods and expand the data availability for emission inventories.Implications: Ammonia emissions must be measured to determine emission factors and reporting national inventories. Measurements from structures like farms and industrial plants are complex due to the many different emitting surfaces and the building configuration leading to a poor data availability. Micrometeorological methods provide high resolution emission data from the entire structure, but suffer from uncertainties, as the instruments must be placed at a distance from the structure resulting in a greater loss of the emitted ammonia via dry deposition before it reaches the measurement. This study constrains such emission measurements from a dairy housing and wastewater treatment plant by applying a simple correction to account for the deposition loss and compares the results to other methods.

The Microbiology of Biological Soil Crusts

Biological soil crusts are thin, inconspicuous communities along the soil atmosphere ecotone that, until recently, were unrecognized by ecologists and even more so by microbiologists. In its broadest meaning, the term biological soil crust (or biocrust) encompasses a variety of communities that develop on soil surfaces and are powered by photosynthetic primary producers other than higher plants: cyanobacteria, microalgae, and cryptogams like lichens and mosses. Arid land biocrusts are the most studied, but biocrusts also exist in other settings where plant development is constrained. The minimal requirement is that light impinge directly on the soil; this is impeded by the accumulation of plant litter where plants abound. Since scientists started paying attention, much has been learned about their microbial communities, their composition, ecological extent, and biogeochemical roles, about how they alter the physical behavior of soils, and even how they inform an understanding of early life on land. This has opened new avenues for ecological restoration and agriculture.

Unveiling the underestimated direct emissions of nitrous acid (HONO)

Gaseous nitrous acid (HONO) is a critical source of hydroxyl radicals (OH) in the troposphere. While both direct and secondary sources contribute to atmospheric HONO, direct emissions have traditionally been considered minor contributors. In this study, we developed δ15N and δ18O isotopic fingerprints to identify six direct HONO emission sources and conducted a 1-y case study on the isotopic composition of atmospheric HONO at rural and urban sites. Interestingly, we identified that livestock farming is a previously overlooked direct source of HONO and determined its HONO to ammonia (NH3) emission ratio. Additionally, our results revealed that spatial and temporal variations in atmospheric HONO isotopic composition can be partially attributed to direct emissions. Through a detailed HONO budget analysis incorporating agricultural sources, we found that direct HONO emissions accounted for 39~45% of HONO production in rural areas across different seasons. The findings were further confirmed by chemistry transport model simulations, highlighting the significance of direct HONO emissions and their impact on air quality in the North China Plain. These findings provide compelling evidence that direct HONO emissions play a more substantial role in contributing to atmospheric HONO than previously believed. Moreover, the δ15N and δ18O isotopic fingerprints developed in this study may serve as a valuable tool for further research on the atmospheric chemistry of reactive nitrogen gases.

Purification effects show seed and root mucilage's ability to respond to changing rhizosphere conditions

Mucilage, a polysaccharide-containing hydrogel, is hypothesized to play a key role in the rhizosphere as a self-organized system because it may vary its supramolecular structure with changes in the surrounding solution. However, there is currently limited research on how these changes are reflected in the physical properties of real mucilage. This study examines the role of solutes in maize root, wheat root, chia seed, and flax seed mucilage in relation to their physical properties. Two purification methods, dialysis and ethanol precipitation, were applied to determine the purification yield, cation content, pH, electrical conductivity, surface tension, viscosity, transverse 1 H relaxation time, and contact angle after drying of mucilage before and after purification. The two seed mucilage types contain more polar polymers that are connected to larger assemblies via multivalent cation crosslinks, resulting in a denser network. This is reflected in higher viscosity and water retention ability compared to root mucilage. Seed mucilage also contains fewer surfactants, making them better wettable after drying compared to the two root mucilage types. The root mucilage types, on the other hand, contain smaller polymers or polymer assemblies and become less wettable after drying. However, wettability not only depends on the amount of surfactants but also on their mobility, as well as the strength and mesh size of the network structure. The changes in physical properties and cation composition observed after ethanol precipitation and dialysis suggest that the polymer network of seed mucilage is more stable and specialized in protecting the seeds from unfavorable environmental conditions. In contrast, root mucilage is characterized by fewer cationic interactions and its network relies more on hydrophobic interactions. This allows root mucilage to be more flexible in responding to changing environmental conditions, facilitating nutrient and water exchange between root surfaces and the rhizosphere soil.

MgO nanocube hydroxylation by nanometric water films

Hydrophilic nanosized minerals exposed to air moisture host thin water films that are key drivers of reactions of interest in nature and technology. Water films can trigger irreversible mineralogical transformations, and control chemical fluxes across networks of aggregated nanomaterials. Using X-ray diffraction, vibrational spectroscopy, electron microscopy, and (micro)gravimetry, we tracked water film-driven transformations of periclase (MgO) nanocubes to brucite (Mg(OH)₂) nanosheets. We show that three monolayer-thick water films first triggered the nucleation-limited growth of brucite, and that water film loadings continuously increased as newly-formed brucite nanosheets captured air moisture. Small (8 nm-wide) nanocubes were completely converted to brucite under this regime while growth on larger (32 nm-wide) nanocubes transitioned to a diffusion-limited regime when (∼0.9 nm-thick) brucite nanocoatings began hampering the flux of reactive species. We also show that intra- and inter-particle microporosity hosted a hydration network that sustained GPa-level crystallization pressures, compressing interlayer brucite spacing during growth. This was prevalent in aggregated 8 nm wide nanocubes, which formed a maze-like network of slit-shaped pores. By resolving the impact of nanocube size and microporosity on reaction yields and crystallization pressures, this work provides new insight into the study of mineralogical transformations induced by nanometric water films. Our findings can be applied to structurally related minerals important to nature and technology, as well as to advance ideas on crystal growth under nanoconfinement.

Atmospheric HONO formation during and after the Spring Festival holidays in a coastal city of China

Nitrous acid (HONO) is an important source of hydrogen oxides (HOx), which affects air quality, the atmospheric oxidation capacity, and human health. Here, we present ambient measurements of the HONO concentrations in Zhuhai, a coastal city in Southern China, from February 7 to March 15, 2021. The campaign was classified into two periods during (P1) and after (P2) the Spring Festival holidays. The average HONO mixing ratio during P2 (1.19 ± 0.85 ppbv) was much higher than that during P1 (0.24 ± 0.18 ppbv), likely due to the contribution of homogeneous HONO formation. During nighttime, the heterogeneous conversion rate during P2 (0.0089/hr) was considerably higher than that during P1 (0.0057/hr), suggesting a higher heterogeneous NO₂ conversion potential. However, the heterogeneous NO₂ conversion was the dominant way during P1 with a high percentage of 88%, while comparable ratios of heterogeneous and homogeneous formation were found (54% vs. 46%) during P2, indicating that the homogeneous formation was also important during P2. During daytime, homogeneous reaction was the major known pathway, with a contribution of 16% during P1 and 27% during P2, leaving large unknown HONO sources which reasonably correlated with the photo-enhanced NO₂ conversion. Two case scenarios were additionally explored, showing that there might be a primary emission source during one scenario (February 17-18) and vehicle emissions might be the major unknown HONO source for another scenario (March 3-5). The results suggest that large unknown daytime sources still exist which need more future ambient and laboratory studies.

Water Adsorption on Mica Surfaces with Hydrophilicity Tuned by Counterion Types (Na, K, and Cs) and Structural Fluorination

The stability of adsorbed water films on mineral surfaces has far-reaching implications in the Earth, environmental, and materials sciences. Here, we use the basal plane of phlogopite mica, an atomically smooth surface of a natural mineral, to investigate water film structure and stability as a function of two features that modulate surface hydrophilicity: the type of adsorbed counterions (Na, K, and Cs) and the substitution of structural OH groups by F atoms. We use molecular dynamics simulations combined with in situ high-resolution X-ray reflectivity to examine surface hydration over a range of water loadings, from the adsorption of isolated water molecules to the formation of clusters and films. We identify four regimes characterized by distinct adsorption energetics and different sensitivities to cation type and mineral fluorination: from 0 to 0.5 monolayer film thickness, the hydration of adsorbed ions; from 0.5 to 1 monolayer, the hydration of uncharged regions of the siloxane surface; from 1 to 1.5 monolayer, the attachment of isolated water molecules on the surface of the first monolayer; and for >1.5 monolayer, the formation of an incipient electrical double layer at the mineral-water interface.

Reactive Nitrogen Hotspots Related to Microscale Heterogeneity in Biological Soil Crusts

Biocrusts covering drylands account for major fractions of terrestrial biological nitrogen fixation and release large amounts of gaseous reactive nitrogen (N_r) as nitrous acid (HONO) and nitric oxide (NO). Recent investigations suggested that aerobic and anaerobic microbial nitrogen transformations occur simultaneously upon desiccation of biocrusts, but the spatio-temporal distribution of seemingly contradictory processes remained unclear. Here, we explore small-scale gradients in chemical concentrations related to structural characteristics and organism distribution. X-ray microtomography and fluorescence microscopy revealed mixed pore size structures, where photoautotrophs and cyanobacterial polysaccharides clustered irregularly in the uppermost millimeter. Microsensor measurements showed strong gradients of pH, oxygen, and nitrite, nitrate, and ammonium ion concentrations at micrometer scales in both vertical and lateral directions. Initial oxygen saturation was mostly low (∼30%) at full water holding capacity, suggesting widely anoxic conditions, and increased rapidly upon desiccation. Nitrite concentrations (∼6 to 800 μM) and pH values (∼6.5 to 9.5) were highest around 70% WHC. During further desiccation they decreased, while emissions of HONO and NO increased, reaching maximum values around 20% WHC. Our results illustrate simultaneous, spatially separated aerobic and anaerobic nitrogen transformations, which are critical for N_r emissions, but might be impacted by future global change and land management.

Impact of Fungal Hyphae on Growth and Dispersal of Obligate Anaerobic Bacteria in Aerated Habitats

Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes. Here, we analyzed whether and to which degree hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of the obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, microscopy, and metabolite analysis revealed the formation and persistence of anoxic circum hyphal niches, allowing for spore germination, growth, and fermentative activity of the obligate anaerobe in an otherwise inhabitable environment. Hypoxic liquid films containing 80% ± 10% of atmospheric oxygen saturation around single air-exposed hyphae thereby allowed for efficient clostridial dispersal amid spatially separated (>0.5 cm) anoxic sites. Hyphae hence may serve as good networks for the activity and spatial organization of obligate anaerobic bacteria in oxygenated heterogeneous environments such as soil.

pH Distribution along Growing Fungal Hyphae at Microscale

Creating unique microenvironments, hyphal surfaces and their surroundings allow for spatially distinct microbial interactions and functions at the microscale. Using a microfluidic system and pH-sensitive whole-cell bioreporters (Synechocystis sp. PCC6803) attached to hyphae, we spatially resolved the pH along surfaces of growing hyphae of the basidiomycete Coprinopsis cinerea. Time-lapse microscopy analysis of ratiometric fluorescence signals of >2400 individual bioreporters revealed an overall pH drop from 6.3 ± 0.4 (n = 2441) to 5.0 ± 0.3 (n = 2497) within 7 h after pH bioreporter loading to hyphal surfaces. The pH along hyphal surfaces varied significantly (p < 0.05), with pH at hyphal tips being on average ~0.8 pH units lower than at more mature hyphal parts near the entrance of the microfluidic observation chamber. Our data represent the first dynamic in vitro analysis of surface pH along growing hyphae at the micrometre scale. Such knowledge may improve our understanding of spatial, pH-dependent hyphal processes, such as the degradation of organic matter or mineral weathering.

Climate warming, but not Spartina alterniflora invasion, enhances wetland soil HONO and NOx emissions

Climate warming and invasive plant growth (plant invasion) may aggravate air pollution by affecting soil nitrogen (N) cycling and the emissions of reactive N gases, such as nitrous acid (HONO) and nitrogen oxides (NO_x). However, little is known about the response of soil NO_y (HONO + NO_x) emissions and microbial functional genes to the interaction of climate warming and plant invasion. Here, we found that experimental warming (approximately 1.5 °C), but not Spartina alterniflora invasion, increased NO_y emissions (0-140 ng N m^-2 s^-1) of treated wetland soils by 4-10 fold. Warming also decreased soil archaeal and fungal richness and diversity, shifted their community structure (e.g., decreased the archaeal classes Thermoplasmata and Iainarchaeia, and increased the archaeal genus Candidatus Nitrosoarchaeum, and the fungal classes Saccharomycetes and Tritirachiomycetes), and decreased the overall abundance of soil N cycling genes. Structural equation modeling revealed that warming-associated changes in edaphic factors and the microbial N cycling potential are responsible for the observed increase in soil NO_y emissions. Collectively, the results showed that climate warming accelerates soil N cycling by stimulating large soil HONO and NO_x emissions, and influences air quality by contributing to atmospheric reactive N and ozone cycling.

Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions

Biological soil crusts (biocrusts) release the reactive nitrogen gases (N_r) nitrous acid (HONO) and nitric oxide (NO) into the atmosphere, but the underlying microbial process controls have not yet been resolved. In this study, we analyzed the activity of microbial consortia relevant in N_r emissions during desiccation using transcriptome and proteome profiling and fluorescence in situ hybridization. We observed that < 30 min after wetting, genes encoding for all relevant nitrogen (N) cycling processes were expressed. The most abundant transcriptionally active N-transforming microorganisms in the investigated biocrusts were affiliated with Rhodobacteraceae, Enterobacteriaceae, and Pseudomonadaceae within the Alpha- and Gammaproteobacteria. Upon desiccation, the nitrite (NO₂^-) content of the biocrusts increased significantly, which was not the case when microbial activity was inhibited. Our results confirm that NO₂^- is the key precursor for biocrust emissions of HONO and NO. This NO₂^- accumulation likely involves two processes related to the transition from oxygen-limited to oxic conditions in the course of desiccation: (i) a differential regulation of the expression of denitrification genes; and (ii) a physiological response of ammonia-oxidizing organisms to changing oxygen conditions. Thus, our findings suggest that the activity of N-cycling microorganisms determines the process rates and overall quantity of N_r emissions.

Key Role of Equilibrium HONO Concentration over Soil in Quantifying Soil-Atmosphere HONO Fluxes

Nitrous acid (HONO) is an important component of the global nitrogen cycle and can regulate the atmospheric oxidative capacity. Soil is an important source of HONO. [HONO]*, the equilibrium gas-phase concentration over the aqueous solution of nitrous acid in the soil, has been suggested as a key parameter for quantifying soil fluxes of HONO. However, [HONO]* has not yet been well-validated and quantified. Here, we present a method to retrieve [HONO]* by conducting controlled dynamic chamber experiments with soil samples applied with different HONO concentrations at the chamber inlet. We show a bi-directional soil-atmosphere exchange of HONO and confirm the existence of [HONO]* over soil: when [HONO]* is higher than the atmospheric HONO concentration, HONO will be released from soil; otherwise, HONO will be deposited. We demonstrate that [HONO]* is a soil characteristic, which is independent of HONO concentrations in the chamber but varies with different soil water contents. We illustrate the robustness of using [HONO]* for quantifying soil fluxes of HONO, whereas the laboratory-determined chamber HONO fluxes can largely deviate from those in the real world for the same soil sample. This work advances the understanding of the soil-atmosphere exchange of HONO and the evaluation of its impact on the atmospheric oxidizing capacity.

Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport

Nitrogen (N) is an essential nutrient that limits plant growth in many ecosystems. Here we investigate an overlooked component of the terrestrial N cycle - subsurface ammonia (NH₃ ) gas transport and its contribution to plant and mycorrhizal N acquisition. We used controlled mesocosms, soil incubations, stable isotopes, and imaging to investigate edaphic drivers of NH₃ gas efflux, track lateral subsurface N transport originating from ¹⁵ NH₃ gas or ¹⁵ N-enriched organic matter, and assess plant and mycorrhizal N assimilation from this gaseous transport pathway. NH₃ is released from soil organic matter, travels belowground, and contributes to root and fungal N content. Abiotic soil properties (pH and texture) influence the quantity of NH₃ available for subsurface transport. Mutualisms with arbuscular mycorrhizal (AM) fungi can substantially increase plant NH₃ -N uptake. The grass Brachypodium distachyon acquired 6-9% of total plant N from organic matter-N that traveled as a gas belowground. Colonization by the AM fungus Rhizophagus irregularis was associated with a two-fold increase in total plant N acquisition from subsurface NH₃ gas. NH₃ gas transport and uptake pathways may be fundamentally different from those of more commonly studied soil N species and warrant further research.

A walk on the dirt: soil microbial forensics from ecological theory to the crime lab

Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.

Coupled Air Quality and Boundary-Layer Meteorology in Western U.S. Basins during Winter: Design and Rationale for a Comprehensive Study

Wintertime episodes of high aerosol concentrations occur frequently in urban and agricultural basins and valleys worldwide. These episodes often arise following development of persistent cold-air pools (PCAPs) that limit mixing and modify chemistry. While field campaigns targeting either basin meteorology or wintertime pollution chemistry have been conducted, coupling between interconnected chemical and meteorological processes remains an insufficiently studied research area. Gaps in understanding the coupled chemical-meteorological interactions that drive high pollution events make identification of the most effective air-basin specific emission control strategies challenging. To address this, a September 2019 workshop occurred with the goal of planning a future research campaign to investigate air quality in Western U.S. basins. Approximately 120 people participated, representing 50 institutions and 5 countries. Workshop participants outlined the rationale and design for a comprehensive wintertime study that would couple atmospheric chemistry and boundary-layer and complex-terrain meteorology within western U.S. basins. Participants concluded the study should focus on two regions with contrasting aerosol chemistry: three populated valleys within Utah (Salt Lake, Utah, and Cache Valleys) and the San Joaquin Valley in California. This paper describes the scientific rationale for a campaign that will acquire chemical and meteorological datasets using airborne platforms with extensive range, coupled to surface-based measurements focusing on sampling within the near-surface boundary layer, and transport and mixing processes within this layer, with high vertical resolution at a number of representative sites. No prior wintertime basin-focused campaign has provided the breadth of observations necessary to characterize the meteorological-chemical linkages outlined here, nor to validate complex processes within coupled atmosphere-chemistry models.

N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers

Nitrous oxide (N₂O) and NO_y (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO₂)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N₂O and NO_y emissions_. Yet, little is known about HONO and NO₂ production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N₂O and NO_y production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NO_y production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N₂O based on results from NH₂OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH₂OH) and NO transformation enzymatic activities may lead to a buildup of NH₂OH/NO which can abiotically react to N₂O ; iv) collectively confirm restrained N₂O and NO_y emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.

Direct observation of anisotropic growth of water films on minerals driven by defects and surface tension

Knowledge of the occurrences of water films on minerals is critical for global biogeochemical and atmospheric processes, including element cycling and ice nucleation. The underlying mechanisms controlling water film growth are, however, misunderstood. Using infrared nanospectroscopy, amplitude-modulated atomic force microscopy, and molecular simulations, we show how water films grow from water vapor on hydrophilic mineral nanoparticles. We imaged films with up to four water layers that grow anisotropically over a single face. Growth usually begins from the near edges of a face where defects preferentially capture water vapor. Thicker films produced by condensation cooling completely engulf nanoparticles and form thicker menisci over defects. The high surface tension of water smooths film surfaces and produces films of inhomogeneous thickness. Nanoscale topography and film surface energy thereby control anisotropic distributions and thicknesses of water films on hydrophilic mineral nanoparticles.