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

Reducing Soil-Emitted Nitrous Acid as a Feasible Strategy for Tackling Ozone Pollution

Severe ozone (O3) pollution has been a major air quality issue and affects environmental sustainability in China. Conventional mitigation strategies focusing on reducing volatile organic compounds and nitrogen oxides (NOx) remain complex and challenging. Here, through field flux measurements and laboratory simulations, we observe substantial nitrous acid (HONO) emissions (FHONO) enhanced by nitrogen fertilizer application at an agricultural site. The observed FHONO significantly improves model performance in predicting atmospheric HONO and leads to regional O3 increases by 37%. We also demonstrate the significant potential of nitrification inhibitors in reducing emissions of reactive nitrogen, including HONO and NOx, by as much as 90%, as well as greenhouse gases like nitrous oxide by up to 60%. Our findings introduce a feasible concept for mitigating O3 pollution: reducing soil HONO emissions. Hence, this study has important implications for policy decisions related to the control of O3 pollution and climate change.

Critical steps in an environmental metaproteomics workflow

Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

Survival and rapid resuscitation permit limited productivity in desert microbial communities

Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.

Reshaping the plastisphere upon deposition: Promote N2O production through affecting sediment microbial communities in aquaculture pond

Microplastics (MPs) could provide vector for microorganisms to form biofilm (plastisphere), but the shaping process of MPs biofilm and its effects on the structure and function of sedimentary microbial communities especially in aquaculture environments are not reported. For this, we incubated MPs biofilm in situ in an aquaculture pond and established a sediment microcosm with plastisphere. We found that the formation of MPs biofilm in surface water was basically stable after 30 d incubation, but the biofilm communities were reshaped after deposition for another 30 d, because they were more similar to plastisphere communities incubated directly within sediment but not surface water. Moreover, microbial communities of MPs-contaminated sediment were altered, which was mainly driven by the biofilm communities present on MPs, because they but not sediment communities in proximity to MPs had a more pronounced separation from the control sediment communities. In the presence of MPs, increased sediment nitrification, denitrification and N2O production rates were observed. The K00371 (NO2-⇋NO3-) pathway and elevated abundance of nxrB and narH genes were screened by metagenomic analysis. Based on structural equation model, two key bacteria (Alphaproteobacteria bacterium and Rhodobacteraceae bacterium) associated with N2O production were further identified. Overall, the settling of MPs could reshape the original biofilm and promote N2O production by selectively elevating sedimental microorganisms and functional genes in aquaculture pond.

Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands

Drylands refer to water scarcity and low nutrient levels, and their plant and biocrust distribution is highly diverse, making the microbial processes that shape dryland functionality particularly unique compared to other ecosystems. Drylands are constraint for sustainable agriculture and risk for food security, and expected to increase over time. Nitrous oxide (N2O), a potent greenhouse gas with ozone reduction potential, is significantly influenced by microbial communities in drylands. However, our understanding of the biological mechanisms and processes behind N2O emissions in these areas is limited, despite the fact that they highly account for total gaseous nitrogen (N) emissions on Earth. This review aims to illustrate the important biological pathways and microbial players that regulate N2O emissions in drylands, and explores how these pathways might be influenced by global changes for example N deposition, extreme weather events, and climate warming. Additionally, we propose a theoretical framework for manipulating the dryland microbial community to effectively reduce N2O emissions using evolving techniques that offer inordinate specificity and efficacy. By combining expertise from different disciplines, these exertions will facilitate the advancement of innovative and environmentally friendly microbiome-based solutions for future climate change vindication approaches.

Severe photochemical pollution formation associated with strong HONO emissions from dew and guttation evaporation

The unknown daytime source of HONO has been extensively investigated due to unexplained atmospheric oxidation capacity and current modelling bias, especially during cold seasons. In this study, abrupt morning increases in atmospheric HONO at a rural site in the North China Plain (NCP) were observed almost on daily basis, which were closely linked to simultaneous rises in atmospheric water vapor content and NH3 concentrations. Dew and guttation water formation was frequently observed on wheat leaves, from which water samples were taken and chemically analyzed for the first time. Results confirmed that such natural processes likely governed the daily nighttime deposition and daytime release of HONO and NH3, which have not been considered in the numerous HONO budget studies investigating its large missing daytime source in the NCP. The dissolved HONO and NH3 in leaf surface water droplets reached 1.4 and 23 mg L-1 during the morning on average, resulting in averaged atmospheric HONO and NH3 increases of 0.89 ± 0.61 and 43.7 ± 29.3 ppb during morning hours, with relative increases of 186 ± 212 % and 233 ± 252 %, respectively. The high atmospheric oxidation capacity contained within HONO was stored in near surface liquid water (such as dew, guttation and soil surface water) during nighttime, which prevented its atmospheric dispersion after sunset and protected it from photodissociation during early morning hours. HONO was released in a blast during later hours with stronger solar radiation, which triggered and then accelerated daytime photochemistry through the rapid photolysis of HONO and subsequent OH production, especially under high RH conditions, forming severe secondary gaseous and particulate pollution. Results of this study demonstrate that global ecosystems might play significant roles in atmospheric photochemistry through nighttime dew formation and guttation processes.

Removal of nitric oxide in bioreactors: a review on the pathways, governing factors and mathematical modelling

The constant surge in nitric oxide in the atmosphere results in severe environmental degradation, negatively impacting human health and ecosystems, and is presently a global concern. Widely used physicochemical technologies for nitric oxide (NO) removal comes with high installation and operational costs and the production of secondary pollutants. Thus, biological treatment has been emphasized over the last two decades, but the poor solubility of NO in water makes it a challenging issue. The present article reviews the various technical aspects of biological treatment of nitric oxide, including the removal pathways and reactor configurations involved in the process. The most widely used technologies in this regard are chemical adsorption processes followed by biological reactors like biofilters, biotrickling filters and membrane bioreactors that enhance NO solubility and offer the flexibility and scope of further improvement in process design. The effect of various experimental and operational parameters on NO removal, including pH, carbon source, gas flow rate, gas residence time and presence of inhibitory components in the flue gas, is also discussed along with the developed mathematical models for predicting NO removal in a biological treatment system. There is an extensive scope of investigation regarding the development of an economical system to remove NO, and an exhaustive model that would optimize the process considering maximum practical parameters encountered during such operation. A detailed discussion made in this article gives a proper insight into all these areas.

Bacterial denitrification drives elevated N2O emissions in arid southern California drylands

Soils are the largest source of atmospheric nitrous oxide (N2O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N2O-producing process, yet, among the largest N2O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N2O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N2O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ15Nbulk = 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N2O emissions by 59%. Our results suggest that despite extreme environmental conditions-months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%-bacterial denitrifiers can account for most of the N2O emitted when dry soils are wetted.

Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments

Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.

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.

Nitrate with enriched heavy oxygen isotope linked to changes in nitrogen source and transformation as groundwater table rises

Nitrate is a significant constituent of the total nitrogen pool in shallow aquifers and poses an escalating threat to groundwater resources, making it crucial to comprehend the source, conversion, and elimination of nitrogen using appropriate techniques. Although dual-isotope dynamics in nitrate have been widely used, uncertainties remain regarding the asynchronously temporal changes in δ¹⁸O-NO₃^- and δ¹⁵N-NO₃^- observed in hypoxic aquifers. This study aimed to investigate changes in nitrogen sources and transformations using temporal changes in field-based NO₃^- isotopic composition, hydro-chemical variables, and environmental DNA profiling, as the groundwater table varied. The results showed that the larger enrichment in δ¹⁸O-NO₃^- (+13‰) compared with δ¹⁵N-NO₃^- (-2‰) on average during groundwater table rise was due to a combination of factors, including high ¹⁸O-based atmospheric N deposition, canopies nitrification, and soil nitrification transported vertically by rainfalls, and ¹⁸O-enriched O₂ produced through microbial and root respiration within denitrification. The strong association between functional gene abundance and nitrogen-related indicators suggests that anammox was actively processed with nitrification but in small bacterial population during groundwater table rise. Furthermore, bacterial species associated with nitrogen-associated gradients provided insight into subsurface nitrogen transformation, with Burkholderiaceae species and Pseudorhodobacter potentially serving as bioindicators of denitrification, while Candidatus Nitrotogn represents soil nitrification. Fluctuating groundwater tables can cause shifts in hydro-chemical and isotopic composition, which in turn can indicate changes in nitrogen sources and transformations. These changes can be used to improve input sources for mixture models and aid in microbial remediation of nitrate.

Eukaryotes contribute more than bacteria to the recovery of freshwater ecosystem functions under different drought durations

Global climate change mostly impacts river ecosystems by affecting microbial biodiversity and ecological functions. Considering the high functional redundancy of microorganisms, the unknown relationship between biodiversity and ecosystem functions obstructs river ecological research, especially under the influence of increasing weather extremes, such as in intermittent rivers and ephemeral streams (IRES). Herein, dry-wet alternation experiments were conducted in artificial stream channels for 25 and 90 days of drought, both followed by 20 days of rewetting. The dynamic recovery of microbial biodiversity and ecosystem functions (represented by ecosystem metabolism and denitrification rate) were determined to analyse biodiversity-ecosystem-function (BEF) relationships after different drought durations. There was a significant difference between bacterial and eukaryotic biodiversity recovery after drought. Eukaryotic biodiversity was more sensitive to drought duration than bacterial, and the eukaryotic network was more stable under dry-wet alternations. Based on the establishment of partial least squares path models, we found that eukaryotic biodiversity has a stronger effect on ecosystem functions than bacteria after long-term drought. Indeed, this work represents a significant step forward for further research on the ecosystem functions of IRES, especially emphasizing the importance of eukaryotic biodiversity in the BEF relationship.

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.

What is a biocrust? A refined, contemporary definition for a broadening research community

Studies of biological soil crusts (biocrusts) have proliferated over the last few decades. The biocrust literature has broadened, with more studies assessing and describing the function of a variety of biocrust communities in a broad range of biomes and habitats and across a large spectrum of disciplines, and also by the incorporation of biocrusts into global perspectives and biogeochemical models. As the number of biocrust researchers increases, along with the scope of soil communities defined as ‘biocrust’, it is worth asking whether we all share a clear, universal, and fully articulated definition of what constitutes a biocrust. In this review, we synthesize the literature with the views of new and experienced biocrust researchers, to provide a refined and fully elaborated definition of biocrusts. In doing so, we illustrate the ecological relevance and ecosystem services provided by them. We demonstrate that biocrusts are defined by four distinct elements: physical structure, functional characteristics, habitat, and taxonomic composition. We describe outgroups, which have some, but not all, of the characteristics necessary to be fully consistent with our definition and thus would not be considered biocrusts. We also summarize the wide variety of different types of communities that fall under our definition of biocrusts, in the process of highlighting their global distribution. Finally, we suggest the universal use of the Belnap, Büdel & Lange definition, with minor modifications: Biological soil crusts (biocrusts) result from an intimate association between soil particles and differing proportions of photoautotrophic (e.g. cyanobacteria, algae, lichens, bryophytes) and heterotrophic (e.g. bacteria, fungi, archaea) organisms, which live within, or immediately on top of, the uppermost millimetres of soil. Soil particles are aggregated through the presence and activity of these often extremotolerant biota that desiccate regularly, and the resultant living crust covers the surface of the ground as a coherent layer. With this detailed definition of biocrusts, illustrating their ecological functions and widespread distribution, we hope to stimulate interest in biocrust research and inform various stakeholders (e.g. land managers, land users) on their overall importance to ecosystem and Earth system functioning.

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.