Controls and Adaptive Management of Nitrification in Agricultural Soils

Effects of Biochar on Cadmium Availability, Nitrification and Microbial Communities in Soils with Varied pH Levels

Cadmium (Cd) contamination poses severe threats to agricultural productivity and ecosystem health. Biochar has shown promise in immobilizing Cd and enhancing microbial functions, yet its pH-dependent mechanisms remain underexplored. This study aimed to elucidate pH-dependent variations in biochar-mediated cadmium (Cd) immobilization efficiency, nitrification activity, and bacterial community diversity across soils of contrasting pH levels, with mechanistic insights into the synergistic interplay between biochar properties and soil pH. Real-time quantitative PCR (qPCR) and high-throughput sequencing were used to investigate the effects of a 1% (w/w) biochar amendment on ammonia-oxidizing microorganism abundance and microbial diversity in neutral Shandong soil (SD, pH 7.46) and acidic Yunnan soil (YN, pH 5.88). In neutral SD soil, available Cd decreased from 0.22 mg kg-1 (day 0) to 0.1 mg kg-1 (day 56) and stabilized, accompanied by insignificant changes in ammonia-oxidizing bacteria (AOB) abundance. However, nitrification activity was enhanced through the enrichment of Nitrospira (nitrite-oxidizing bacteria within Nitrospirales and Nitrospiraceae). In acidic YN soil, biochar reduced available Cd by 53.37% over 56 days, concurrent with a 34.28% increase in AOB amoA gene abundance (predominantly Nitrosomonadales), driving pH-dependent nitrification enhancement. These findings demonstrated that biochar efficacy was critically modulated by soil pH; the acidic soils require higher biochar dosages (>1% w/w, adjusted to local soil properties and agronomic conditions) for optimal Cd immobilization. Meanwhile, pH-specific nitrifier taxa (Nitrosomonadales in acidic vs. Nitrospira in neutral soils) underpinned biochar-induced nitrification dynamics. The study provided a mechanistic framework for tailoring biochar remediation strategies to soil pH gradients, emphasizing the synergistic regulation of Cd immobilization and microbial nitrogen cycling.

The invisible architects: microbial communities and their transformative role in soil health and global climate changes

During the last decades, substantial advancements have been made in identifying soil characteristics that impact the composition of the soil microbiome. However, the impacts of microorganisms on their respective soil habitats have received less attention, with the majority of prior research focusing on the contributions of microbes to the dynamics of soil carbon and nitrogen. Soil microbiome plays a critical role in soil habitats by influencing soil fertility, crop yields, and biotic and abiotic stress tolerance. In addition to their roles in nutrient cycling and organic matter transformations, soil microorganisms affect the soil environment via many biochemical and biophysical mechanisms. For instance, the soil microbiome plays an essential role in soil mechanical stability and pore connectivity and regulates the flow of nutrients, oxygen, and water. Similarly, soil microbiomes perform various critical functions in an ecosystem, which leads to carbon stabilization for a long time and could serve as microbiome engineering targets for global climate change mitigation. In this review, considering soil structure, hydrology, and chemistry, we outline how microorganisms alter the soil ecosystem. Further, this study investigates the mechanisms by which feedback loops can be generated between microorganisms and soil. Moreover, we analyze the potential of microbially mediated modifications of soil properties as a viable strategy to address soil threats and global climate challenges. In addition, the current study propose a deep learning-based approach to develop a synthetic microbial consortium to improve soil health and mitigate climate change.

Irrigation System, Rather than Nitrogen Fertilizer Application, Affects the Quantities of Functional Genes Related to N2O Production in Potato Cropping

The spatial and temporal distribution of water and nitrogen supply affects soil-borne nitrous oxide (N2O) emissions. In this study, the effects of different irrigation technologies (no irrigation, sprinkler irrigation and drip irrigation) and nitrogen (N) application types (no fertilizer, broadcasted and within irrigation water) on N2O flux rates and the quantities of functional genes involved in the N cycle in potato cropping were investigated over an entire season. The volume of irrigation water affected microbial N2O production, with the highest N2O flux rates found under sprinkler irrigation conditions, followed by drip and no irrigation. Nitrifier denitrification was identified as the potential pre-dominant pathway stimulated by fluctuations in aerobic-anaerobic soil conditions, especially under sprinkler irrigation. Regarding the different N application types, increased N use efficiency under fertigation was expected. However, N2O flux rates were not significantly reduced compared to broadcasted N application under drip irrigation. On average, the N2O fluxes were higher during the first half of the season, which was accompanied by a low N use efficiency of the potato crops. Potato crops mainly require N at later growth stages. Due to the different water and nutrient demand of potatoes, an adjusted application of fertilizer and water based on crop demand could reduce N2O emissions.

Plant growth strategies and microbial contributions to ecosystem nitrogen retention along a soil acidification gradient

Nitrogen (N) retention is a critical ecosystem function associated with sustainable N supply. Lack of experimental evidence limits our understanding of how grassland N retention can vary with soil acidification. A 15N-labeling experiment was conducted for 2 years to quantify N retention by soil pathways and plant functional groups across a soil-acidification gradient in a meadow. The 15N added to the ecosystem was mainly intercepted by the soil (up to 87.3%). Within the soil, 15N recovery in ammonium, dissolved organic N, microbial biomass, and amino sugars (a proxy for microbial necromass) represented approximately 46% of soil-retained 15N. 15N recovery in these N fractions increased with acidification, highlighting the complexity of microbial N transformations that affect ecosystem N retention. Plant 15N-retention increased in sedges, decreased in forbs, and was unaffected in grasses with acidification, reflecting their divergent associations with mycorrhizas and sensitivities to soil acidification. Soil microbial biomass was the key variable delineating soil N retention, while sedges were critical for plant N retention, resulting in a clear trade-off and competition in 15N retention between the two compartments. Overall, acidification might curb N losses by strengthening microbial retention and shifting plant N retention among different plant growth strategies.

Differential Responses of Soil Ammonia-oxidizing Bacterial and Archaeal Communities to Land-use Changes in Zambia

Soil nutrient loss from intensive farming is a critical issue in sub-Saharan Africa that affects food security. While soil microbial nitrification supplies available nitrogen, excessive nitrification leads to nitrogen loss. However, the species driving nitrification and their functions in this region remain largely unknown. Therefore, we investigated the responses of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to land-use changes in Zambia and their relationship with nitrification potential. Soil samples were collected from three sites in Zambia that all had neighboring natural and farmed (maize) lands. We measured nitrification potential, quantified AOB and AOA, and analyzed these communities by targeting the ammonia monooxygenase subunit A (amoA) gene, which encodes a key enzyme in nitrification. Nitrification potential was 1.51-fold higher in farmlands than in natural lands. AOB abundance tended to be greater in farmlands, whereas AOA abundance was smaller. Farming changed the AOB community structure, increasing Nitrosospira cluster 3a.2 at the three sites, while minor site-specific responses were also observed. In contrast, the AOA community structure was not significantly different between land uses, but varied among sites, with cluster NS-ζ being more prominent in one site with neutral soil (pH 7.64) than in the other sites (pH 5.70 and 5.71). These results suggest that AOA species were generally vulnerable to farming, decreasing in abundance without structural changes, while some AOB species increased, driving changes in their community structure. These insights are fundamental for understanding soil nitrogen depletion due to microbial changes under farming and are crucial for developing sustainable land-use practices in sub-Saharan Africa.

"Ca. Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres

Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper (Capsicum anuum L.) and ginseng plants (Panax ginseng C.A. Mey.) compared to bulk soil not penetrated by roots. While the abundance of total AOA decreased in the rhizosphere soils, AOA related to "Candidatus Nitrosocosmicus," which harbor gene encoding manganese catalase (MnKat) in contrast to most other AOA, dominated the AOA community in the rhizosphere soils. For both plant species, the ratio of copy numbers of the AOA MnKat gene to the amoA gene (encoding the ammonia monooxygenase subunit A) was significantly higher in the rhizospheres than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. Due to their abundance, "Ca. Nitrosocosmicus" members can be considered important players mediating the nitrification process in rhizospheres. The dominance of this MnKat-containing AOA in rhizospheres of agriculturally important plants hints at a previously overlooked AOA-plant interaction.

IMPORTANCE

Ammonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the "Ca. Nitrosocosmicus" clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that "Ca. Nitrosocosmicus" may be an important clade of AOA with potential AOA-plant interaction.

Microbes in Agriculture: Prospects and Constraints to Their Wider Adoption and Utilization in Nutrient-Poor Environments

Microbes such as bacteria and fungi play important roles in nutrient cycling in soils, often leading to the bioavailability of metabolically important mineral elements such as nitrogen (N), phosphorus (P), iron (Fe), and zinc (Zn). Examples of microbes with beneficial traits for plant growth promotion include mycorrhizal fungi, associative diazotrophs, and the N2-fixing rhizobia belonging to the α, β and γ class of Proteobacteria. Mycorrhizal fungi generally contribute to increasing the surface area of soil-root interface for optimum nutrient uptake by plants. However, when transformed into bacteroids inside root nodules, rhizobia also convert N2 gas in air into ammonia for use by the bacteria and their host plant. Thus, nodulated legumes can meet a high proportion of their N requirements from N2 fixation. The percentage of legume N derived from atmospheric N2 fixation varies with crop species and genotype, with reported values ranging from 50-97%, 24-67%, 66-86% 27-92%, 50-92%, and 40-75% for soybean (Gycine max), groundnut (Arachis hypogea), mung bean (Vigna radiata), pigeon pea (Cajanus cajan), cowpea (Vigna unguiculata), and Kersting's groundnut (Macrotyloma geocarpum), respectively. This suggests that N2-fixing legumes require little or no N fertilizer for growth and grain yield when grown under field conditions. Even cereals and other species obtain a substantial proportion of their N nutrition from associative and endophytic N2-fixing bacteria. For example, about 12-33% of maize N requirement can be obtained from their association with Pseudomonas, Hebaspirillum, Azospirillum, and Brevundioronas, while cucumber can obtain 12.9-20.9% from its interaction with Paenebacillus beijingensis BJ-18. Exploiting the plant growth-promoting traits of soil microbes for increased crop productivity without any negative impact on the environment is the basis of green agriculture which is done through the use of biofertilizers. Either alone or in combination with other synergistic rhizobacteria, rhizobia and arbuscular mycorrhizal (AM) fungi have been widely used in agriculture, often increasing crop yields but with occasional failures due to the use of poor-quality inoculants, and wrong application techniques. This review explores the literature regarding the plant growth-promoting traits of soil microbes, and also highlights the bottle-necks in tapping this potential for sustainable agriculture.

Nitrite manipulation in water by structure change of plasma electrolysis reactor

In this study, experimental reactors for cathodic nitrogen plasma electrolysis were designed by the composition of galvanic (voltaic) and electrolytic cells with wide and narrow connectors filled with tap water and agar solutions. The designed reactor can be used to simultaneously perform and manage nitrification in acidic and alkaline environments. According to the reactor's performance, it can be installed on the irrigation system and used depending on the soil pH of the fields for delivering water and nitrogen species that are effective in growth. The nitrification process was investigated by choosing the optimal reactor with a wide connector based on different changes in oxidation-reduction potential and pH on the anode and cathode sides. The nitrite concentration changed directly with ammonium and nitrate concentrations on the cathode side. It changed inversely and directly with ammonium and nitrate concentrations on the anode side respectively. Nitrite concentration decreased from 5.387 ppm with water connector, to 0.326 ppm with 20% agar solution, and 0.314 ppm with 30% agar solution connectors on the anode side. It increased from 0 ppm to 0.191 ppm with a water connector, 0.405 ppm with 20% agar solution, and 7.454 ppm with 30% agar solution connectors on the cathode side.

Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems

The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Feature-specific nutrient management of onion (Allium cepa) using machine learning and compositional methods

While onion cultivars, irrigation and soil and crop management have been given much attention in Brazil to boost onion yields, nutrient management at field scale is still challenging due to large dosage uncertainty. Our objective was to develop an accurate feature-based fertilization model for onion crops. We assembled climatic, edaphic, and managerial features as well as tissue tests into a database of 1182 observations from multi-environment fertilizer trials conducted during 13 years in southern Brazil. The complexity of onion cropping systems was captured by machine learning (ML) methods. The RReliefF ranking algorithm showed that the split-N dosage and soil tests for micronutrients and S were the most relevant features to predict bulb yield. The decision-tree random forest and extreme gradient boosting models were accurate to predict bulb yield from the relevant predictors (R2 > 90%). As shown by the gain ratio, foliar nutrient standards for nutritionally balanced and high-yielding specimens producing > 50 Mg bulb ha-1 set apart by the ML classification models differed among cultivars. Cultivar × environment interactions support documenting local nutrient diagnosis. The split-N dosage was the most relevant controllable feature to run future universality tests set to assess models' ability to generalize to growers' fields.

Agritech to Tame the Nitrogen Cycle

While the Haber-Bosch process for N-fixation has enabled a steady food supply for half of humanity, substantial use of synthetic fertilizers has caused a radical unevenness in the global N-cycle. The resulting increases in nitrate production and greenhouse gas (GHG) emissions have contributed to eutrophication of both ground and surface waters, the growth of oxygen minimum zones in coastal regions, ozone depletion, and rising global temperatures. As stated by the Food and Agriculture Organization of the United Nations, agriculture releases ∼9.3 Gt CO2 equivalents per year, of which methane (CH4) and nitrous oxide (N2O) account for 5.3 Gt CO2 equivalents. N-pollution and slowing the runaway N-cycle requires a combined effort to replace chemical fertilizers with biological alternatives, which after a 10-yr span of usage could eliminate a minimum of 30% of ag-related GHG emissions (∼1.59 Gt), protect waterways from nitrate pollution, and protect soils from further deterioration. Agritech solutions include bringing biological fertilizers and biological nitrification inhibitors to the marketplace to reduce the microbial conversion of fertilizer nitrogen into GHGs and other toxic intermediates. Worldwide adoption of these plant-derived molecules will substantially elevate nitrogen use efficiency by crops while blocking the dominant source of N2O to the atmosphere and simultaneously protecting the biological CH4 sink. Additional agritech solutions to curtail N-pollution, soil erosion, and deterioration of freshwater supplies include soil-free aquaponics systems that utilize improved microbial inocula to enhance nitrogen use efficiency without GHG production. With adequate and timely investment and scale-up, microbe-based agritech solutions emphasizing N-cycling processes can dramatically reduce GHG emissions on short time lines.

Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity

Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.

Nitrogen (N) "supplementation, slow release, and retention" strategy improves N use efficiency via the synergistic effect of biochar, nitrogen-fixing bacteria, and dicyandiamide

Irrational nitrogen (N) fertilizer management and application practices have led to a range of ecological and environmental problems that seriously threaten food security. In this study, an effective N fertilizer management strategy was established for improving N fertilizer utilization efficiency (NUE). Biochar, N2-fixing bacteria (Enterobacter cloacae), and a nitrification inhibitor (dicyandiamide, DCD) were simultaneously added to the soil during maize cultivation. The goal was to increase soil ammonium nitrogen content and NUE by regulating the relative abundance, enzyme activity, and functional gene expression of N conversion-related soil microbes. Biochar combined with E. cloacae and DCD significantly increased soil N content, and the NUE reached 46.69 %. The relative abundance of Burkholderia and Bradyrhizobium and the activity of nitrogenase increased significantly during biological N2 fixation. Further, the abundance of the nifH gene was significantly up-regulated. The relative abundance of Sphingomonas, Pseudomonas, Nitrospira, and Castellaniella and the activities of ammonia monooxygenase and nitrate reductase decreased significantly during nitrification and denitrification. Moreover, the abundance of the genes amoA and narG was significantly down-regulated. Correlation analyses showed that the increase in soil N2 fixation and the suppression of nitrification and denitrification reactions were the key contributors to the increase in soil N content and NUE. Biochar combined with E. cloacae and DCD synergistically enabled the supplementation, slow release, and retention of N, thus providing adequate N for maize growth. Thus, the combination of biochar, E. cloacae, and DCD is effective for mitigating the irrational application of N fertilizers and reducing N pollution.

A systematic review of life-cycle GHG emissions from intensive pig farming: Accounting and mitigation

Pork accounts for approximately 35 % of the global meat supply, with approximately 747 million tons of CO2e greenhouse gas (GHG) emissions annually. To meet the increasing demand for pork, intensive farming is becoming the priority rearing system owing to its higher productivity. Given the climate transformation ambitions of the pig industry but the lack of knowledge and data, we conducted a systematic review of studies published in the period of 2010-2022 from a life-cycle perspective, with a focus on greenhouse gas emissions accounting and mitigation. The significant variations in systematic harmonized global warming intensities (GWIs) can be primarily attributed to differences in accounting approaches, activity data, technologies and geographical conditions. To understand more, we broke down the entire life cycle and revealed the underlying reasons for modelling mechanisms and data from the main emitters (e.g., feeding, pig rearing, and manure management). These findings are expected to support and improve the transparency, consistency, and comprehensiveness of life-cycle GHG emissions accounting in pig farming. Potential mitigation measures were also reviewed and discussed to provide insights to support the sustainable development of the pig industry.

Study on the effectiveness and mechanism of a sustainable dual slow-release model to improve N utilization efficiency and reduce N pollution in black soil

Long-term intensive cultivation has led to serious N loss and low N fertilizer utilization efficiency (NUE) in black soil areas. The lost N is not only a waste of resources but also a serious pollution threat to the environment, leading to the decline in water quality and food safety and the greenhouse effect. In the present study, a stable dual slow-release model, CPCS-Urea, was prepared by in situ polymerization using nitrapyrin, urea and melamine-formaldehyde resin as raw materials. The effect of the dual slow-release model was systematically evaluated using two consecutive years of field experiments. Five treatments were established in the field experiment: no N fertilizer (N0), urea (N180), 1 % CPEC-Urea, 0.5 % CPCS-Urea, and 1 % CPCS-Urea. The results showed that the new dual slow-release CPCS-Urea model outperformed both the use of urea and the traditional slow-release CPEC-Urea model in reducing N losses and improving NUE. The application of CPCS-Urea reduced nitrate (NO3-) leaching by 28.2 %-47.2 % and N2O emissions by 36.5 %-42.4 % and increased NUE by 20.7 %-28.5 % compared to urea application. The CPCS-Urea model modulated the activity of ammonia-oxidizing bacteria (AOB) and dissimilatory nitrate reduction to ammonium (DNRA) bacteria in soil, showing a significant decrease in AOB activity and an increase in DNRA activity. This results in a lower soil NO3--N yield and a 53.1 %-72.0 % increase in NH4+-N content, providing sufficient N for the entire growth and development cycle of maize. In short, the dual slow-release CPCS-Urea model has great application prospects for promoting agricultural development in black soil areas.

Isolation of a Moderately Acidophilic Nitrobacter from a Nitrifying Community Supplied with Urea

Nitrite-oxidizing bacteria (NOB), which perform the second step of aerobic nitrification, play an important role in soil. In the present study, we report a novel isolate from agricultural soil affiliated with the genus Nitrobacter and its physiological characteristics. We sampled the surface soil of a vegetable field and obtained mixed culture A31 using the most probable number (MPN) method with inorganic medium containing 0.75‍ ‍mM urea (pH 5.5). The dilution-extinction procedure on culture A31 led to the isolation of a strain that was designated as Nitrobacter sp. A67. The nxrB1 gene sequence of Nitrobacter sp. A67 (302 bp) was classified into Cluster 5, and the highest sequence identity was 96.10% with Nitrobacter sp. BS5/19. The NO2- oxidation activity of Nitrobacter sp. A67 was investigated at various pH. The optimum pH for NO2- oxidation was 5.8-6.4. This result indicates that Nitrobacter sp. A67 is a moderately acidophilic nitrite-oxidizing bacterium.

Investigating microbial and environmental drivers of nitrification in alkaline forest soil

Ammonia oxidation is a key step in the biogeochemical cycling of nitrogen, and soils are important ecosystems for nitrogen flux globally. Approximately 25% of the world's soils are alkaline. While nitrification has been studied more extensively in agricultural alkaline soils, less is known about natural, unfertilized alkaline soils. In this study, microorganisms responsible for ammonia oxidation and several environmental factors (season, temperature, ammonia concentration, and moisture content) known to affect nitrification were studied in an alkaline forest soil with a pH ranging from 8.36 to 8.77. Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea, and comammox were present, and AOB belonging to genera Nitrosospira and Nitrosomonas, originally comprising <0.01% of the total bacterial community, responded rapidly to ammonia addition to the soil. No significant difference was observed in nitrification rates between seasons, but there was a significant difference between in situ field nitrification rates and rates in laboratory microcosms. Surprisingly, nitrification took place under many of the tested conditions, but there was no detectable increase in the abundance of any recognizable group of ammonia oxidizers. This study raises questions about the role of low-abundance microorganisms in microbial processes and of situations where zero or very low microbial growth coincides with metabolic activity. In addition, this study provides insights into nitrification in unfertilized alkaline soil and supports previous studies, which found that AOB play an important role in alkaline soils supplemented with ammonia, including agricultural ecosystems.

Nitrite stimulates HONO and NOx but not N2O emissions in Chinese agricultural soils during nitrification

The long-lived greenhouse gas nitrous oxide (N2O) and short-lived reactive nitrogen (Nr) gases such as ammonia (NH3), nitrous acid (HONO), and nitrogen oxides (NOx) are produced and emitted from fertilized soils and play a critical role for climate warming and air quality. However, only few studies have quantified the production and emission potentials for long- and short-lived gaseous nitrogen (N) species simultaneously in agricultural soils. To link the gaseous N species to intermediate N compounds [ammonium (NH4+), hydroxylamine (NH2OH), and nitrite (NO2-)] and estimate their temperature change potential, ex-situ dry-out experiments were conducted with three Chinese agricultural soils. We found that HONO and NOx (NO + NO2) emissions mainly depend on NO2-, while NH3 and N2O emissions are stimulated by NH4+ and NH2OH, respectively. Addition of 3,4-dimethylpyrazole phosphate (DMPP) and acetylene significantly reduced HONO and NOx emissions, while NH3 emissions were significantly enhanced in an alkaline Fluvo-aquic soil. These results suggested that ammonia-oxidizing bacteria (AOB) and complete ammonia-oxidizing bacteria (comammox Nitrospira) dominate HONO and NOx emissions in the alkaline Fluvo-aquic soil, while ammonia-oxidizing archaea (AOA) are dominant in the acidic Mollisol. DMPP effectively mitigated the warming effect in the Fluvo-aquic soil and the Ultisol. In conclusion, our findings highlight NO2- significantly stimulates HONO and NOx emissions from dryland agricultural soils, dominated by nitrification. In addition, subtle differences of soil NH3, N2O, HONO, and NOx emissions indicated different N turnover processes, and should be considered in biogeochemical and atmospheric chemistry models.

Combining frass and fatty acid co-products derived from Black soldier fly larvae farming shows potential as a slow release fertiliser

Use of black soldier fly larvae (BSFL) to process large volumes of organic waste is an emerging industry to produce protein. A co-product of this industry, the larval faeces (frass), has potential to be used as an organic fertiliser in a circular economy. However, BSFL frass has a high ammonium (N-NH4+) content which could result in nitrogen (N) loss following its application to land. One solution is to process the frass by combining it with solid fatty acids (FA) that have previously been used to manufacture slow-release inorganic fertilisers. We investigated the slow-releasing effect of N after combining BSFL frass with three FAs - lauric, myristic and stearic acid. Soil was amended with the three forms of FA processed (FA-P) frass, unprocessed frass or a control and incubated for 28 days. The impact of treatments on soil properties and soil bacterial communities were characterised during the incubation. Lower N-NH4+ concentrations occurred in soil treated with FA-P frass compared to unprocessed frass, and N-NH4+ release was slowest for lauric acid processed frass. Initially, all frass treatments caused a large shift in the soil bacterial community towards a dominance of fast-growing r-strategists that were correlated with increased organic carbon levels. FA-P frass appeared to enhance the immobilisation of N-NH4+ (from frass) by diverting it into microbial biomass. Unprocessed and stearic acid processed frass became enriched by slow-growing K-strategist bacteria at the latter stages of the incubation. Consequently, when frass was combined with FAs, FA chain length played an important role in regulating the composition of r-/K- strategists in soil and N and carbon cycling. Modifying frass with FAs could be developed into a slow release fertiliser leading to reduced soil N loss, improved fertiliser use efficiency, increased profitability and lower production costs.

Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy

Background

Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.

Results

We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.

Conclusions

The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.

Biological and chemical nitrification inhibitors exhibited different effects on soil gross N nitrification rate and N2O production: a 15N microcosm study

Nitrification inhibitors (NIs) are considered as an effective strategy for reducing nitrification rate and related environmental nitrogen (N) loss. However, whether plant-derived biological NIs had an advantage over chemical NIs in simultaneously inhibiting nitrification rate and N2O production remains unclear. Here, we conducted an aerobic 15N microcosmic incubation experiment to compare the effects of a biological NI (methyl 3-(4-hydroxyphenyl) propionate, MHPP) with three chemical NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), dicyandiamide (DCD), and 3,4-dimethylpyrazole phosphate (DMPP) on (i) gross N mineralization and nitrification rate and (ii) the relative importance of nitrification and denitrification in N2O emission in a calcareous soil. The results showed that DMPP significantly inhibited m_gross rate (P < 0.05), whereas DCD, nitrapyrin, and MHPP only numerically inhibited it. Gross N nitrification (n_gross) rates were inhibited by 9.48% in the DCD treatment to 51.5% in the nitrapyrin treatment. Chemical NIs primarily affected the amoA gene abundance of ammonia-oxidizing bacteria (AOB), whereas biological NIs affected the amoA gene abundance of ammonia-oxidizing archaea (AOA) and AOB. AOB's community composition was more susceptible to NIs than AOA, and NIs mainly targeted Nitrosospira clusters of AOB. Chemical NIs of DCD, DMPP, and nitrapyrin proportionally reduced N2O production from nitrification and denitrification. However, the biological NI MHPP stimulated short-term N2O emission and increased the proportion of N2O from denitrification. Our findings showed that the influence of NIs on gross N mineralization rate (m_gross) was dependent on the NI type. MHPP exhibited a moderate n_gross inhibitory capacity compared with the three chemical NIs. The mechanisms of chemical and biological NIs inhibiting n_gross can be partly attributed to changes in the abundance and community of ammonia oxidizers. A more comprehensive evaluation is needed to determine whether biological NIs have advantages over chemical NIs in inhibiting greenhouse gas emissions.

Incubation study on remediation of nitrate-contaminated soil by Chroococcus sp

The possibility of using the non-nitrogen-fixing cyanobacterium (Chroococcus sp.) for the reduction of soil nitrate contamination was tested through Petri dish experiments. The application of 0.03, 0.05 and 0.08 mg/cm2 Chroococcus sp. efficiently removed NO3--N from the soil through assimilation of nitrate nutrient and promotion of soil denitrification. At the optimal application dose of 0.05 mg/cm2, 44.06%, 36.89% and 36.17% of NO3--N were removed at initial NO3--N concentrations of 60, 90 and 120 mg/kg, respectively. The polysaccharides released by Chroococcus sp. acted as carbon sources for bacterial denitrification and facilitated the reduction of soil salinity, which significantly (p < 0.05) stimulated the growth of denitrifying bacteria (Hyphomicrobium denitrificans and Hyphomicrobium sp.) as well as significantly (p < 0.05) elevated the activities of nitrate reductase and nitrite reductase by 1.07-1.23 and 1.15-1.22 times, respectively. The application of Chroococcus sp. promoted the dominance of Nocardioides maradonensis in soil microbial community, which resulted in elevated phosphatase activity and increased available phosphorus content. The application of Chroococcus sp. positively regulated the growth of soil bacteria belonging to the genera Chitinophaga, Prevotella and Tumebacillus, which may contribute to increased soil fertility through the production of beneficial enzymes such as invertase, urease and catalase. To date, this is the first study verifying the remediation effect of non-nitrogen-fixing cyanobacteria on nitrate-contaminated soil.

The Legacy of Plant Invasion: Impacts on Soil Nitrification and Management Implications

Plant invasions can have long-lasting impacts on soil nitrification, which plays a critical role in nutrient cycling and plant growth. This review examines the legacy effects of plant invasion on soil nitrification, focusing on the underlying mechanisms, context dependence, and implications for management. We synthesize literature on the positive, negative and neutral legacy effects of plant invasion on soil nitrification, highlighting the complexity of these effects and the need for further research to fully understand them. Positive legacy effects include increased soil microbial biomass or activity, potentially enhancing nutrient availability for plants. However, negative legacy effects, like reduced nitrifier abundance, can result in decreased soil nitrification rates and nutrient availability. In some cases, changes to nitrification during active invasion appear transitory after the removal of invasive plants, indicating neutral short-term legacies. We discuss the context dependence of legacy effects considering factors, including location, specific invasive plant species, and other environmental conditions. Furthermore, we discuss the implications of these legacy effects for management and restoration strategies, such as the removal or control of invasive plants, and potential approaches for restoring ecosystems with legacy effects on soil nitrification. Finally, we highlight future research directions, including further investigation into the mechanisms and context dependence of legacy effects, and the role of plant-microbe interactions. Overall, this review provides insights into the legacy effects of plant invasion on soil nitrification and their implications for ecosystems.

An In Silico Analysis of Synthetic and Natural Compounds as Inhibitors of Nitrous Oxide Reductase (N2OR) and Nitrite Reductase (NIR)

Nitrification inhibitors are recognized as a key approach that decreases the denitrification process to inhibit the loss of nitrogen to the atmosphere in the form of N2O. Targeting denitrification microbes directly could be one of the mitigation approaches. However, minimal attempts have been devoted towards the development of denitrification inhibitors. In this study, we aimed to investigate the molecular docking behavior of the nitrous oxide reductase (N2OR) and nitrite reductase (NIR) involved in the microbial denitrification pathway. Specifically, in silico screening was performed to detect the inhibitors of nitrous oxide reductase (N2OR) and nitrite reductase (NIR) using the PatchDock tool. Additionally, a toxicity analysis based on insecticide-likeness, Bee-Tox screening, and a STITCH analysis were performed using the SwissADME, Bee-Tox, and pkCSM free online servers, respectively. Among the twenty-two compounds tested, nine ligands were predicted to comply well with the TICE rule. Furthermore, the Bee-Tox screening revealed that none of the selected 22 ligands exhibited toxicity on honey bees. The STITCH analysis showed that two ligands, namely procyanidin B2 and thiocyanate, have interactions with both the Paracoccus denitrificans and Hyphomicrobium denitrificans microbial proteins. The molecular docking results indicated that ammonia exhibited the second least atomic contact energy (ACE) of -15.83 kcal/mol with Paracoccus denitrificans nitrous oxide reductase (N2OR) and an ACE of -15.20 kcal/mol with Hyphomicrobium denitrificans nitrite reductase (NIR). The inhibition of both the target enzymes (N2OR and NIR) supports the view of a low denitrification property and suggests the potential future applications of natural/synthetic compounds as significant nitrification inhibitors.

Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge

Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.

Post-Intensification Poaceae Cropping: Declining Soil, Unfilled Grain Potential, Time to Act

The status and sustainability of Poaceae crops, wheat and barley, were examined in an Atlantic zone climate. Intensification had caused yield to rise 3-fold over the last 50 years but had also degraded soil and biodiversity. Soil carbon and nitrogen were compared with current growth and yield of crops. The yield gap was estimated and options considered for raising yield. Organic carbon stores in the soil (C-soil) ranged from <2% in intensified systems growing long-season wheat to >4% in low-input, short-season barley and grass. Carbon acquisition by crops (C-crop) was driven mainly by length of season and nitrogen input. The highest C-crop was 8320 kg ha^-1 C in long-season wheat supported by >250 kg ha^-1 mineral N fertiliser and the lowest 1420 kg ha^-1 in short-season barley fertilised by livestock grazing. Sites were quantified in terms of the ratio C-crop to C-soil, the latter estimated as the mass of carbon in the upper 0.25 m of soil. C-crop/C-soil was <1% for barley in low-input systems, indicating the potential of the region for long-term carbon sequestration. In contrast, C-crop/C-soil was >10% in high-input wheat, indicating vulnerability of the soil to continued severe annual disturbance. The yield gap between the current average and the highest attainable yield was quantified in terms of the proportion of grain sink that was unfilled. Intensification had raised yield through a 3- to 4-fold increase in grain number per unit field area, but the potential grain sink was still much higher than the current average yield. Filling the yield gap may be possible but could only be achieved with a major rise in applied nitrogen. Sustainability in Poaceae cropping now faces conflicting demands: (a) conserving and regenerating soil carbon stores in high-input systems, (b) reducing GHG emissions and other pollution from N fertiliser, (c) maintaining the yield or closing the yield gap, and (d) readjusting production among food, feed, and alcohol markets. Current cropping systems are unlikely to satisfy these demands. Transitions are needed to alternative systems based on agroecological management and biological nitrogen fixation.

Unraveling mechanisms behind reduced nitrate leaching with graphite nanomaterials addition with fertilizers in soil column experiments

Overuse or mistimed application of nitrogen fertilizer can cause nitrate contamination in groundwater and surrounding surface waters. Previous greenhouse studies have explored the use of graphene nanomaterials, including graphite nano additive (GNA), to reduce nitrate leaching in an agricultural soil while growing lettuce crops. To investigate the mechanism of GNA addition in suppressing nitrate leaching, we conducted soil column experiments using native agricultural soils under saturated or unsaturated flow conditions to simulate varied irrigation. We investigated the effects of temperature (4 °C compared with 20 °C) on microbial activity and dose effect of GNA was also explored (165 mg/kg soil and 1650 mg/kg soil) for biotic soil column experiments whereas a single temperature condition (20 °C) and GNA dose (165 mg/kg soil) was employed for abiotic (autoclaved) soil column experiments. Results showed GNA addition had minimal effects on nitrate leaching in saturated flow soil columns due to short hydraulic residence times (∼3.5 h). In comparison, longer residence times (∼3 d) in unsaturated soil columns reduced nitrate leaching by 25-31% relative to control soil columns without GNA addition. Furthermore, nitrate retention in the soil column was found to be suppressed at 4 °C compared with 20 °C, suggesting a bio-mediated mechanism for GNA addition to reduce nitrate leaching. In addition, the soil dissolved organic matter was found to be associated with nitrate leaching, where less nitrate leaching occurring when higher dissolved organic carbon (DOC) was measured in leachate water. Following studies of adding soil-derived organic carbon (SOC) resulted in greater nitrogen retention in the unsaturated soil columns only when GNA was present. Overall, the results suggest that GNA-amended soil reduces nitrate loss through increased N immobilization in the microbial biomass or loss of N in gaseous phase through enhanced nitrification and denitrification process.

Dissolved biochar fractions and solid biochar particles inhibit soil acidification induced by nitrification through different mechanisms

Biochar can inhibit soil acidification by decreasing the H⁺ input from nitrification and improving soil pH buffering capacity (pHBC). However, biochar is a complex material and the roles of its different components in inhibiting soil acidification induced by nitrification remain unclear. To address this knowledge gap, dissolved biochar fractions (DBC) and solid biochar particles (SBC) were separated and mixed thoroughly with an amended Ultisol. Following a urea addition, the soils were subjected to an incubation study. The results showed that both the DBC and SBC inhibited soil acidification by nitrification. The DBC inhibited soil acidification by decreasing the H⁺ input from nitrification, while SBC enhanced the soil pHBC. The DBC from peanut straw biochar (PBC) and rice straw biochar (RBC) decreased the H⁺ release by 16 % and 18 % at the end of incubation. The decrease in H⁺ release was attributed to the inhibition of soil nitrification and net mineralization caused by the toxicity of the phenols in DBC to soil bacteria. The abundance of ammonia-oxidizing bacteria (AOB) and total bacteria decreased by >60 % in the treatments with DBC. The opposite effects were observed in the treatments with SBC. Soil pHBC increased by 7 % and 19 % after the application of solid RBC and PBC particles, respectively. The abundance of carboxyl on the surface of SBC was mainly responsible for the increase in soil pHBC. Generally, the mixed application of DBC and SBC was more effective at inhibiting soil acidification than their individual applications. The negative impacts of dissolved biochar components on soil microorganisms need to be closely monitored.

Understanding the Mechanisms of Fe Deficiency in the Rhizosphere to Promote Plant Resilience

One of the most significant constraints on agricultural productivity is the low availability of iron (Fe) in soil, which is directly related to biological, physical, and chemical activities in the rhizosphere. The rhizosphere has a high iron requirement due to plant absorption and microorganism density. Plant roots and microbes in the rhizosphere play a significant role in promoting plant iron (Fe) uptake, which impacts plant development and physiology by influencing nutritional, biochemical, and soil components. The concentration of iron accessible to these live organisms in most cultivated soil is quite low due to its solubility being limited by stable oxyhydroxide, hydroxide, and oxides. The dissolution and solubility rates of iron are also significantly affected by soil pH, microbial population, organic matter content, redox processes, and particle size of the soil. In Fe-limiting situations, plants and soil microbes have used active strategies such as acidification, chelation, and reduction, which have an important role to play in enhancing soil iron availability to plants. In response to iron deficiency, plant and soil organisms produce organic (carbohydrates, amino acids, organic acids, phytosiderophores, microbial siderophores, and phenolics) and inorganic (protons) chemicals in the rhizosphere to improve the solubility of poorly accessible Fe pools. The investigation of iron-mediated associations among plants and microorganisms influences plant development and health, providing a distinctive prospect to further our understanding of rhizosphere ecology and iron dynamics. This review clarifies current knowledge of the intricate dynamics of iron with the end goal of presenting an overview of the rhizosphere mechanisms that are involved in the uptake of iron by plants and microorganisms.

Mediation of gaseous emissions and improving plant productivity by DCD and DMPP nitrification inhibitors: Meta-analysis of last three decades

Nitrification inhibitors (NIs), especially dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP), have been extensively investigated to mitigate nitrogen (N) losses from the soil and thus improve crop productivity by enhancing N use efficiency. However, to provide crop and soil-specific guidelines about using these NIs, a quantitative assessment of their efficacy in mitigating gaseous emissions, worth for nitrate leaching, and improving crop productivity under different crops and soils is yet required. Therefore, based upon 146 peer-reviewed research studies, we conducted a meta-analysis to quantify the effect of DCD and DMPP on gaseous emissions, nitrate leaching, soil inorganic N, and crop productivity under different variates. The efficacy of the NIs in reducing the emissions of CO2, CH4, NO, and N2O highly depends on the crop, soil, and experiment types. The comparative efficacy of DCD in reducing N2O emission was higher than the DMPP under maize, grasses, and fallow soils in both organic and chemical fertilizer amended soils. The use of DCD was linked to increased NH3 emission in vegetables, rice, and grasses. Depending upon the crop, soil, and fertilizer type, both the NIs decreased nitrate leaching from soils; however, DMPP was more effective. Nevertheless, the effect of DCD on crop productivity indicators, including N uptake, N use efficiency, and biomass/yield was higher than DMPP due to certain factors. Moreover, among soils, crops, and fertilizer types, the response by plant productivity indicators to the application of NIs ranged between 35 and 43%. Overall, the finding of this meta-analysis strongly suggests the use of DCD and DMPP while considering the crop, fertilizer, and soil types.

Microorganisms carrying nosZ I and nosZ II share similar ecological niches in a subtropical coastal wetland

Nitrous oxide (N₂O) reducers are the only known sink for N₂O and pivotal contributors to N₂O mitigation in terrestrial and water ecosystems. However, the niche preference of nosZ I and nosZ II carrying microorganisms, two divergent clades of N₂O reducers in coastal wetlands, is not yet well documented. In this study, we investigated the abundance, community structure and co-occurrence network of nosZ I and nosZ II carrying microorganisms and their driving factors at three depths in a subtropical coastal wetland with five plant species and a bare tidal flat. The taxonomic identities differed between nosZ I and nosZ II carrying microorganisms, with nosZ I sequences affiliated with Alphaproteobacteria and Betaproteobacteria while nosZ II sequences with Gemmatimonadetes, Verrucomicrobia, Gammaproteobacteria, and Chloroflexi. The abundances of nosZ I and nosZ II decreased with increasing soil depths, and were positively associated with salinity, total carbon (TC) and total nitrogen (TN). Random forest analysis showed that salinity was the strongest predictor for the abundances of nosZ I and nosZ II. Salinity, TC and TN were the major driving forces for the community structure of nosZ I and nosZ II carrying microorganisms. Moreover, co-occurrence analysis showed that 92.2 % of the links between nosZ I and nosZ II were positive, indicating that nosZ I and nosZ II carrying microorganisms likely shared similar ecological niches. Taken together, we provided new evidence that nosZ I and nosZ II carrying microorganisms shared similar ecological niches in a subtropical estuarine wetland, and identified salinity, TC and TN serving as the most important environmental driving forces. This study advances our understanding of the environmental adaptation and niche preference of nosZ I and nosZ II carrying microorganisms in coastal wetlands.

Straw amendment and nitrification inhibitor controlling N losses and immobilization in a soil cooling-warming experiment

It is common practice in agriculture to apply high‑carbon amendments, e.g. straw, or nitrification inhibitors (NI) to reduce soil nitrogen (N) losses. However, little is known on the combined effects of straw and NI and how seasonal soil temperature variations further affect N immobilization. We conducted a 113-day mesocosm experiment with different levels of ¹⁵N-fertilizer application (N0: control; N1: 125 kg N ha^-1; N2: 250 kg N ha^-1) in an agricultural soil, amended with either wheat straw, NI or a combination of both in order to investigate N retention and loss from soil after a cooling-warming phase simulating a seasonal temperature shift, i.e., 30 days cooling phase at 7 °C and 10 days warming phase at 21 °C. Subsequently, soils were planted with barley as phytometers to study ¹⁵N-transfer to a following crop. Straw addition significantly reduced soil N-losses due to microbial N immobilization. Although carbon added as straw led to increased N₂O emissions at high N fertilization, this was partly counterbalanced by NI. Soil cooling-warming strongly increased ammonification (+77 %), while nitrification was suppressed, and straw-induced microbial N immobilization dominated. N immobilized after straw addition was mineralized at the end of the experiment as indicated by structural equation models. Re-mineralization in N2 was sufficient, but still suboptimal in N0 and N1 at critical times of early barley growth. N-use efficiency of the ¹⁵N tracer decreased with fertilization intensity from 50 % in N1 to 35 % in N2, and straw amendment reduced NUE to 25 % at both fertilization rates. Straw amendment was most powerful in reducing N-losses (-41 %), in particular under variable soil temperature conditions, but NI enforced its effects by reducing N₂O emission (-40 %) in N2 treatment. Sufficient N-fertilization coupled with straw application is required to adjust the timely re-mineralization of N for subsequent crops.

Bioengineering Techniques to Improve Nitrogen Transformation and Utilization: Implications for Nitrogen Use Efficiency and Future Sustainable Crop Production

Nitrogen (N) is crucial for plant growth and development, especially in physiological and biochemical processes such as component of different proteins, enzymes, nucleic acids, and plant growth regulators. Six categories, such as transporters, nitrate absorption, signal molecules, amino acid biosynthesis, transcription factors, and miscellaneous genes, broadly encompass the genes regulating NUE in various cereal crops. Herein, we outline detailed research on bioengineering modifications of N metabolism to improve the different crop yields and biomass. We emphasize effective and precise molecular approaches and technologies, including N transporters, transgenics, omics, etc., which are opening up fascinating opportunities for a complete analysis of the molecular elements that contribute to NUE. Moreover, the detection of various types of N compounds and associated signaling pathways within plant organs have been discussed. Finally, we highlight the broader impacts of increasing NUE in crops, crucial for better agricultural yield and in the greater context of global climate change.

A Comparison of Nitrate Release from Zn/Al-, Mg/Al-, and Mg-Zn/Al Layered Double Hydroxides and Composite Beads: Utilization as Slow-Release Fertilizers

Nitrate-loaded Zn/Al, Mg/Al, and Mg-Zn/Al layered double hydroxides (LDHs) were synthesized using the coprecipitation method. The slow-release properties of LDHs were measured in powder form at various pH conditions. Sodium alginate was used to encapsulate Mg/Al LDH to produce composite beads (LB) to further slow down the release of nitrate ions. The prepared LDH samples and LB were characterized by X-ray diffraction, attenuated total reflectance Fourier transform infrared spectroscopy, thermogravimetric analysis, and inductively coupled plasma optical emission spectroscopy. The surface morphologies of LDHs and LB were obtained from scanning electron microscopy analysis. The slow-release properties of the materials were evaluated using a kinetic study of nitrate release in tap water, soil solution, as well as plant growth experiments using coriander (Coriandrum sativum). The nitrate release ability of LDHs and LB was compared with a soluble nitrate source. The plant growth experiments showed that all three LDHs were able to supply an adequate amount of nitrate to the plant similar to the soluble fertilizer while maintaining the availability of nitrate over extended periods. The ability of LDHs to increase soil pH was also demonstrated.

Nitrification rate in dairy cattle urine patches can be inhibited by changing soil bioavailable Cu concentration

Ammonia oxidation to hydroxylamine is catalyzed by the ammonia monooxygenase enzyme and copper (Cu) is a key element for this process. We investigated the effect of soil bioavailable Cu changes induced through the application of Cu-complexing compounds on nitrification rate, ammonia-oxidizing bacteria (AOB) and archaea (AOA) amoA gene abundance, and mineral nitrogen (N) leaching in urine patches using the Manawatu Recent soil. Further, evaluated the combination of organic compound calcium lignosulphonate (LS) with a growth stimulant Gibberellic acid (GA). Treatments were applied in May 2021 as late-autumn treatments: control (no urine), urine-only at 600 kg N ha^-1, urine + dicyandiamide (DCD), urine + co-poly-acrylic-maleic acid (PA-MA), urine + LS, urine + split-application of LS (2LS), and urine + combination of GA plus LS (GA + LS). In addition, another four treatments were applied in July 2021 as mid-winter treatments: control, urine-only at 600 kg N ha^-1, urine + GA, and urine + GA + LS. Soil bioavailable Cu and mineral N leaching were examined during the experimental period. The AOB/AOA amoA genes were quantified using quantitative polymerase chain reaction. Changes in soil bioavailable Cu across treatments correlated with nitrification rate and AOB amoA abundance in late-autumn while the AOA amoA abundance did not change. The reduction in soil bioavailable Cu induced by the PA-MA and 2LS was linked to significant (P < 0.05) reduction in mineral N leaching of 16 and 30%, respectively, relative to the urine-only. The LS did not induce a significant effect on either bioavailable Cu or mineral N leaching relative to urine-only. The GA + LS reduced mineral N leaching by 10% relative to LS in late-autumn, however, there was no significant effect in mid-winter. This study demonstrated that reducing soil bioavailable Cu can be a potential strategy to reduce N leaching from urine patches.

Assessment of the impact of diluted and pretreated olive mill wastewater on the treatment efficiency by infiltration-percolation using natural bio-adsorbents

The current study was carried out to treat the olive mill wastewater (OMW) via infiltration percolation process, using low-cost natural adsorbents that could improve the ability of the system to enhance the disposal rate of elimination of pollutant from the OMW. The experimental pilot was composed of three PVC (polyvinyl chloride) columns with 10 cm in diameter and 110-cm height equipped with lateral air entries. Each column was filled with four layers of 10 cm of a mixture of sand (70%), charcoal (20%) and sawdust (10%) respectively. These layers were alternated by four permeable layers of 10 cm of Pouzzolane. To assess the effect of the pretreatment on the efficiency of the system, three types of OMW were used: raw OMW, diluted OMW with domestic wastewater at 1/1(v/v) ratio and OMW pretreated with lime. For the column feed with raw OMW, an average removal of total COD (41%), dissolved COD (54%), NH4-N (40.25%), NO₃^- (15.76%), total phosphorus (55.63%) and orthophosphate (50.84%) was recorded. The results showed that the column feed with diluted OMW with domestic wastewater was the most efficient one with a removal rate that reached 93.2% of total COD, 86.2% of dissolved COD, 92% of polyphenol, 92% of orthophosphate (OP), 97.2% of total phosphorus (TP) and 81% of NH4-N. The pretreatment of OMW with lime gave the lowest removal rate for all the parameters: total COD (34%), dissolved COD (50%), NH4-N (30%), NO₃^- (- 21%), total phosphorus (15.19%) and orthophosphate (9.04%). This study demonstrated that the dilution is a way to optimize the efficiency of the system of infiltration-percolation in treating the OMW.

Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils

Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.

Micro-fractionation shows microbial community changes in soil particles below 20 μm

Introduction

Micro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.

Methods

We applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; &gt;250 μm, 250–63 μm, 63–20 μm, 20–2 μm, &lt;2 μm, and supernatant).

Results

Overall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the &lt; 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.

Discussion

The observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.

EgNRT2.3 and EgNAR2 expression are controlled by nitrogen deprivation and encode proteins that function as a two-component nitrate uptake system in oil palm

Oil palm (Elaeis guineensis Jacq.) is an important crop for oil and biodiesel production. Oil palm plantations require extensive fertilizer additions to achieve a high yield. Fertilizer application decisions and management for oil palm farming rely on leaf tissue and soil nutrient analyses with little information available to describe the key players for nutrient uptake. A molecular understanding of how nutrients, especially nitrogen (N), are taken up in oil palm is very important to improve fertilizer use and formulation practice in oil palm plantations. In this work, two nitrate uptake genes in oil palm, EgNRT2.3 and EgNAR2, were cloned and characterized. Spatial expression analysis showed high expression of these two genes was mainly found in un-lignified young roots. Interestingly, EgNRT2.3 and EgNAR2 were up-regulated by N deprivation, but their expression pattern depended on the form of N source. Promoter analysis of these two genes confirmed the presence of regulatory elements that support these expression patterns. The Xenopus oocyte assay showed that EgNRT2.3 and EgNAR2 had to act together to take up nitrate. The results suggest that EgNRT2.3 and EgNAR2 act as a two-component nitrate uptake system in oil palm.

Nitrous oxide emission in altered nitrogen cycle and implications for climate change

Natural processes and human activities play a crucial role in changing the nitrogen cycle and increasing nitrous oxide (N₂O) emissions, which are accelerating at an unprecedented rate. N₂O has serious global warming potential (GWP), about 310 times higher than that of carbon dioxide. The food production, transportation, and energy required to sustain a world population of seven billion have required dramatic increases in the consumption of synthetic nitrogen (N) fertilizers and fossil fuels, leading to increased N₂O in air and water. These changes have radically disturbed the nitrogen cycle and reactive nitrogen species, such as nitrous oxide (N₂O), and have impacted the climatic system. Yet, systematic and comprehensive studies on various underlying processes and parameters in the altered nitrogen cycle, and their implications for the climatic system are still lacking. This paper reviews how the nitrogen cycle has been disturbed and altered by anthropogenic activities, with a central focus on potential pathways of N₂O generation. The authors also estimate the N₂O-N emission mainly due to anthropogenic activities will be around 8.316 Tg N₂O-N yr^-1 in 2050. In order to minimize and tackle the N₂O emissions and its consequences on the global ecosystem and climate change, holistic mitigation strategies and diverse adaptations, policy reforms, and public awareness are suggested as vital considerations. This study concludes that rapidly increasing anthropogenic perturbations, the identification of new microbial communities, and their role in mediating biogeochemical processes now shape the modern nitrogen cycle.

Seed endophytic ammonia oxidizing bacteria in Elymus nutans transmit to offspring plants and contribute to nitrification in the root zone

Background

Ammonia oxidizing bacteria (AOB) in soil are of great biological importance as they regulate the cycling of N in agroecosystems. Plants are known to harbor AOB but how they occupy the plant is an unresolved question.

Methods

Metabarcoding studies were carried out using Illumina MiSeq sequencing to test the potential of seed vectored AOB exchange between plants and soil.

Results and discussion

We found 27 sequences associated with AOB strains belonging to the genera Nitrosospira, Nitrosovibrio, and Nitrosomonas inhabiting Elymus nutans seeds collected from four geographically distanced alpine meadows. Nitrosospira multiformis was the most dominant across the four locations. The AOB community in E. nutans seeds was compared with that of the leaves, roots and soil in one location. Soil and seeds harbored a rich but dissimilar AOB community, and Nitrosospira sp. PJA1, Nitrosospira sp. Nsp17 and Nitrosovibrio sp. RY3C were present in all plant parts and soils. When E. nutans seeds were germinated in sterilized growth medium under greenhouse conditions, the AOB in seeds later appeared in leaves, roots and growth medium, and contributed to nitrification. Testing the AOB community of the second-generation seeds confirmed vertical transmission, but low richness was observed.

Conclusion

These results suggest seed vectored AOB may play a critical role in N cycle.

Effect of agricultural activities on surface water quality from páramo ecosystems

Páramos are high mountain ecosystems strategic for water provision in South America. Currently, páramos are under threat due to agricultural intensification that impairs surface water sources. This research analyzed the effect of agriculture (spring onion-Allium fistulosum, potato-Solanum tuberosum, and livestock farming) on water quality in páramo ecosystems. A Hydrographic Unit upstream of the Jordan river catchment (Colombia) was selected and monitored in two different rainfall regimes, following the paired catchments and upstream-downstream approaches to compare water quality from natural and anthropic areas. Twenty-two parameters related to agricultural activities were analyzed (nutrients, salts, organic matter, sediments, and pathogens). The studied agricultural activities increased loads of surface water in quality in nitrates (0.02 to 2.56 mg N-NO₃/L), potassium (0.13 to 1.24 mg K/L), and Escherichia coli (63 to 2718 FCU/100 mL), generating risks on the human health and promoting eutrophication. Total nitrogen and organic matter in the rainy season were higher than dry. BOD₅, COD, turbidity, and E. coli were above international standards for direct human consumption. However, water could be used for irrigation, livestock watering, and aquatic life ambient freshwater. The results show that a small land-use change of almost 15% from natural páramo vegetation to agricultural uses in these ecosystems impairs water quality, limiting its uses, and the need to harmonize small-scale livelihoods in the páramo with the sustainability of ecosystem service provision.

Changes in microbial communities in soil treated with organic or conventional N sources

Despite the extensive use of N fertilizers in agricultural soils, we are yet to fully understand their impact on soil microbial communities that mediate important soil processes. A 3-yr field study was undertaken in Georgia, where sweet corn (Zea mays L.) was grown under conventional or organic systems. Nitrogen (N) was supplied with ammonium sulfate at 112 kg N ha^-1 (AS100) or 224 kg N ha^-1 (AS200) or a combination of poultry litter, cover crop, and blood meal at 112 kg N ha^-1 (PL100) or no N (control). Soil samples were collected from field plots to assess the impact of treatments on bacteria, fungi, and ammonia oxidizers using molecular methods that targeted 16S RNA, ITS2, and amoA genes, respectively. Treatment had significant impact on bacterial but not fungal composition. The AS200 significantly changed the relative abundances of Verrucomicrobia and Acidobacteria and decreased bacterial alpha diversity as compared with control. Beta-diversity analysis showed clear separation of microbial communities in AS200 vs. control and PL100. The abundance of ammonia-oxidizing bacteria (AOB) was more responsive to N input than ammonia oxidizing-archaea. It was also significantly and positively correlated with nitrification potential and soil nitrate with increasing N rates, indicating AOB's dominance in driving nitrification under high N input. Overall, the results indicated that AS200 changed bacterial composition and diversity, suggesting corresponding changes in soil processes related to N mineralization and nitrification. Understanding such changes in microbial communities can help us predict changes in soil processes to adopt sustainable management systems.

Agroecological Management and Increased Grain Legume Area Needed to Meet Nitrogen Reduction Targets for Greenhouse Gas Emissions

The nitrogen applied (N-input) to cropping systems supports a high yield but generates major environmental pollution in the form of greenhouse gas (GHG) emissions and losses to land and water (N-surplus). This paper examines the scope to meet both GHG emission targets and zero N-surplus in high-intensity, mainly cereal, cropping in a region of the Atlantic zone in Europe. A regional survey provides background to crops grown at an experimental farm platform over a run of 5 years. For three main cereal crops under standard management (mean N-input 154 kg ha−1), N-surplus remained well above zero (single year maximum 55% of N-input, five-year mean 27%), but was reduced to near zero by crop diversification (three cereals, one oilseed and one grain legume) and converted to a net nitrogen gain (+39 kg ha−1, 25 crop-years) by implementing low nitrification management in all fields. Up-scaling N-input to the agricultural region indicated the government GHG emissions target of 70% of the 1990 mean could only be met with a combination of low nitrification management and raising the proportion of grain legumes from the current 1–2% to at least 10% at the expense of high-input cereals. Major strategic change in the agri-food system of the region is therefore needed to meet GHG emissions targets.

Effects of biological nitrification inhibitor in regulating NH3 volatilization and fertilizer nitrogen recovery efficiency in soils under rice cropping

Biological nitrification inhibitors are exudates from plant roots that can inhibit nitrification, and have advantages over traditional synthetic nitrification inhibitors. However, our understanding of the effects of biological nitrification inhibitors on nitrogen (N) loss and fertilizer N recovery efficiency in staple food crops is limited. In this study, acidic and calcareous soils were selected, and rice growth pot experiments were conducted to investigate the effects of the biological nitrification inhibitor, methyl 3-(4-hydroxyphenyl) propionate (MHPP) and/or a urease inhibitor (N-[n-butyl], thiophosphoric triamide [NBPT]) on NH₃ volatilization, N leaching, fertilizer N recovery efficiency under a 20% reduction of the conventional N application rate. Our results show that rice yield and fertilizer N recovery efficiency were more sensitive to reduced N application in the calcareous soil than in the acidic soil. MHPP stimulated NH₃ volatilization by 13.2% in acidic soil and 9.06% in calcareous soil but these results were not significant. In the calcareous soil, fertilizer N recovery efficiency significantly increased by 19.3% and 44.4% in the MHPP and NBPT+MHPP groups, respectively, relative to the reduced N treatment, and the rice yield increased by 16.7% in the NBPT+MHPP treatment (P < 0.05). However, such effects were not significant in the acidic soil. MHPP exerted a significant effect on soil ammonia oxidizers, and the response of abundance and community structure of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and total bacteria to MHPP depended on the soil type. MHPP+NBPT reduced NH₃ volatilization, N leaching, and maintaining rice yield for a 20% reduction in conventional N fertilizer application rate. This could represent a viable strategy for more sustainable rice production, despite the inevitable increase in cost for famers.

The Effects of Quinone Imine, a New Potent Nitrification Inhibitor, Dicyandiamide, and Nitrapyrin on Target and Off-Target Soil Microbiota

Dicyandiamide (DCD) and nitrapyrin (NP) are nitrification inhibitors (NIs) used in agriculture for over 40 years. Recently, ethoxyquin (EQ) was proposed as a novel potential NI, acting through its derivative quinone imine (QI). Still, the specific activity of these NIs on the different groups of ammonia-oxidizing microorganisms (AOM), and mostly their effects on other soil microbiota remain unknown. We determined the impact of QI, and comparatively of DCD and NP, applied at two doses (regular versus high), on the function, diversity, and dynamics of target (AOM), functionally associated (nitrite-oxidizing bacteria-NOB), and off-target prokaryotic and fungal communities in two soils mainly differing in pH (5.4 versus 7.9). QI was equally effective to DCD but more effective than NP in inhibiting nitrification in the acidic soil, while in the alkaline soil QI was less efficient than DCD and NP. This was attributed to the higher activity of QI toward AOA prevailing in the acidic soil. All NIs induced significant effects on the composition of the AOB community in both soils, unlike AOA, which were less responsive. Beyond on-target effects, we noted an inhibitory effect of all NIs on the abundance of NOB in the alkaline soil, with Nitrobacter being more sensitive than Nitrospira. QI, unlike the other NIs, induced significant changes in the composition of the bacterial and fungal communities in both soils. Our findings have serious implications for the efficiency and future use of NIs on agriculture and provide unprecedented evidence for the potential off-target effects of NIs on soil microbiota. IMPORTANCE NIs could improve N use efficiency and decelerate N cycling. Still, we know little about their activity on the distinct AOM groups and about their effects on off-target soil microorganisms. Here, we studied the behavior of a new potent NI, QI, compared to established NIs. We show that (i) the variable efficacy of NIs across soils with different pH reflects differences in the inherent specific activity of the NIs to AOA and AOB; (ii) beyond AOM, NIs exhibit negative effects on other nitrifiers, like NOB; (iii) QI was the sole NI that significantly affected prokaryotic and fungal diversity. Our findings (i) highlight the need for novel NI strategies that consider the variable sensitivity of AOM groups to the different NIs (ii) identify QI as a potent AOA inhibitor, and (iii) stress the need for monitoring NIs' impact on off-target soil microorganisms to ensure sustainable N fertilizers use and soil ecosystem functioning.