Biological nitrification inhibition by rice root exudates and its relationship with nitrogen-use efficiency

Benefits and limits of biological nitrification inhibitors for plant nitrogen uptake and the environment

Plant growth and high yields are secured by intensive use of nitrogen (N) fertilizer, which, however, pollutes the environment, especially when N is in the form of nitrate. Ammonium is oxidized to nitrate by nitrifiers, but roots can release biological nitrification inhibitors (BNIs). Under what conditions does root-exudation of BNIs facilitate nitrogen N uptake and reduce pollution by N loss to the environment? We modeled the spatial-temporal dynamics of nitrifiers, ammonium, nitrate, and BNIs around a root and simulated root N uptake and net rhizosphere N loss over the plant's life cycle. We determined the sensitivity of N uptake and loss to variations in the parameter values, testing a broad range of soil-plant-microbial conditions, including concentrations, diffusion, sorption, nitrification, population growth, and uptake kinetics. An increase in BNI exudation reduces net N loss and, under most conditions, increases plant N uptake. BNIs decrease uptake in the case of (1) low ammonium concentrations, (2) high ammonium adsorption to the soil, (3) rapid nitrate- or slow ammonium uptake by the plant, and (4) a slowly growing or (5) fast-declining nitrifier population. Bactericidal inhibitors facilitate uptake more than bacteriostatic ones. Some nitrification, however, is necessary to maximize uptake by both ammonium and nitrate transporter systems. An increase in BNI exudation should be co-selected with improved ammonium uptake. BNIs can reduce N uptake, which may explain why not all species exude BNIs but have a generally positive effect on the environment by increasing rhizosphere N retention.

The impact of microbial community structure changes on the migration and release of typical heavy metal (loid)s during the revegetation process of mercury-thallium mining waste slag

The effect of changes in microbial community structure on the migration and release of toxic heavy metal (loid)s is often ignored in ecological restoration. Here, we investigated a multi-metal (mercury and thallium, Tl) mine waste slag. With particular focus on its strong acidity, poor nutrition, and high toxicity pollution characteristics, we added fish manure and carbonate to the slag as environmental-friendly amendments. On this basis, ryegrass, which is suitable for the remediation of metal waste dumps, was then planted for ecological restoration. We finally explored the influence of changes in microbial community structure on the release of Tl and As in the waste slag during vegetation reconstruction. The results show that the combination of fish manure and carbonate temporarily halted the release of Tl, but subsequently promoted the release of Tl and arsenic (As), which was closely related to changes in the microbial community structure in the waste slag after fish manure and carbonate addition. The main reason for these patterns was that in the early stage of the experiment, Bacillaceae inhibited the release of Tl by secreting extracellular polymeric substances; with increasing time, Actinobacteriota became the dominant bacterium, which promoted the migration and release of Tl by mycelial disintegration of minerals. In addition, the exogenously added organic matter acted as an electron transport medium for reducing microorganisms and thus helped to reduce nitrate or As (Ⅴ) in the substrate, which reduced the redox potential of the waste slag and promoted As release. At the same time, the phylum Firmicutes, including specific dissimilatory As-reducing bacteria that are capable of converting As into a more soluble form, further promoted the release of As. Our findings provide a theoretical basis for guiding the ecological restoration of relevant heavy-metal (loid) mine waste dumps.

Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition

Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.

Biological mitigation of soil nitrous oxide emissions by plant metabolites

Plant metabolites significantly affect soil nitrogen (N) cycling, but their influence on nitrous oxide (N2O) emissions has not been quantitatively analyzed on a global scale. We conduct a comprehensive meta-analysis of 173 observations from 42 articles to evaluate global patterns of and principal factors controlling N2O emissions in the presence of root exudates and extracts. Overall, plant metabolites promoted soil N2O emissions by about 10%. However, the effects of plant metabolites on N2O emissions from soils varied with experimental conditions and properties of both metabolites and soils. Primary metabolites, such as sugars, amino acids, and organic acids, strongly stimulated soil N2O emissions, by an average of 79%, while secondary metabolites, such as phenolics, terpenoids, and flavonoids, often characterized as both biological nitrification inhibitors (BNIs) and biological denitrification inhibitors (BDIs), reduced soil N2O emissions by an average of 41%. The emission mitigation effects of BNIs/BDIs were closely associated with soil texture and pH, increasing with increasing soil clay content and soil pH on acidic and neutral soils, and with decreasing soil pH on alkaline soils. We furthermore present soil incubation experiments that show that three secondary metabolite types act as BNIs to reduce N2O emissions by 32%-45%, while three primary metabolite classes possess a stimulatory effect of 56%-63%, confirming the results of the meta-analysis. Our results highlight the potential role and application range of specific secondary metabolites in biomitigation of global N2O emissions and provide new biological parameters for N2O emission models that should help improve the accuracy of model predictions.

Cadmium induced changes in rhizosphere microecology to enhance Cd intake by Ligusticum sinense cv. Chuanxiong

As the most famous and widely used traditional Chinese medicine (TCM), Ligusticum sinense cv. Chuanxiong (L. Chuaniong) has been affected by cadmium (Cd) exceeding with high ability of Cd accumulation. There is relatively little research on Cd absorption and storage process in L. Chuanxiong, which is an important reason for the poor remediation efficiency. Hence, this study takes L. Chuanxiong as the point of penetration to explore how L. Chuanxiong affects rhizobacteria through root exudates to alter soil Cd intake, as well as to explore the migration and storage of Cd in its body with 0.10 (T0), 5.00 (T5), 10.00 (T10) mg/kg Cd contaminations. The results showed that the relative abundance of amino acids and phospholipids secreted from L. Chuanxiong root noticeably increased with increasing Cd levels, which directly activated soil Cd or extremely significantly (P < 0.01) recruited bacteria such as Bacillus, Arthrobacter to indirectly increase Cd availability. Under the interaction of root exudates and rhizobacteria, Cd bioavailability increased by 80.00% in rhizosphere soil and Cd accumulation in L. Chuanxiong increased 5.44-6.65 mg/kg. Cd subcellular distribution analysis demonstrated that Cd was mainly stored in the root (10-fold more than in the leaf), whose Cd content was cytoderm>cytoplasm>organelle in tissues. The sequential extraction results found that non-soluble phosphate and protein-chelated Cd dominated (85.00-90.00%) in the cell, while Cd cheated with alcohol soluble protein, amino acid salts, water-soluble organic acid in cell was minimal (5.50%). The phenomenon indicated that L. Chuanxiong fixed Cd in root (the medical part) with low translocation ability. This study can provide theoretical support for the high-quality production of L. Chuanxiong and other root medical plant in heavy metal influenced sites.

Plasma membrane H+-ATPases in mineral nutrition and crop improvement

Plasma membrane H+-ATPases (PMAs) pump H+ out of the cytoplasm by consuming ATP to generate a membrane potential and proton motive force for the transmembrane transport of nutrients into and out of plant cells. PMAs are involved in nutrient acquisition by regulating root growth, nutrient uptake, and translocation, as well as the establishment of symbiosis with arbuscular mycorrhizas. Under nutrient stresses, PMAs are activated to pump more H+ and promote organic anion excretion, thus improving nutrient availability in the rhizosphere. Herein we review recent progress in the physiological functions and the underlying molecular mechanisms of PMAs in the efficient acquisition and utilization of various nutrients in plants. We also discuss perspectives for the application of PMAs in improving crop production and quality.

Nitrification Control by Plants and Preference for Ammonium versus Nitrate: Positive Feedbacks Increase Productivity but Undermine Resilience

AbstractSome plants, via their action on microorganisms, control soil nitrification (i.e., the transformation of ammonium into nitrate). We model how the covariation between plant control of nitrification and preference for ammonium versus nitrate impacts ecosystem properties such as productivity, nitrogen (N) losses, and overall resilience. We show that the control of nitrification can maximize productivity by minimizing total inorganic N losses. We initially predicted that plants with an ammonium preference should achieve the highest biomass when inhibiting nitrification, and conversely that plants preferring nitrate should achieve the highest biomass by stimulating nitrification. With a parametrization derived from the Lamto savanna (Ivory Coast), we find that productivity is maximal for plants that slightly prefer ammonium and inhibit nitrification. Such situations, however, lead to strong positive feedbacks that can cause abrupt shifts from a highly to a lowly productive ecosystem. The comparison with other parameter sets (Pawnee short-grass prairie [United States], intensively cultivated field, and a hypothetical parameter set in which ammonium is highly volatilized and nitrate inputs are high) shows that strategies yielding the highest biomass may be counterintuitive (i.e., preferring nitrate but inhibiting nitrification). We argue that the level of control yielding the highest productivity depends on ecosystem properties (quantity of N deposition, leaching rates, and baseline nitrification rates), not only preference. Finally, while contrasting N preferences offer, as expected, the possibility of coexistence through niche partitioning, we stress how control of nitrification can be framed as a niche construction process that adds an additional dimension to coexistence conditions.

Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates

Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.

Reducing greenhouse gas intensity using a mixture of controlled-release urea and common urea combining suitable maize varieties in a summer maize system

The one-time application of common urea blended with controlled-release urea (CRU) is considered effective for improving nitrogen use efficiency and grain yield and reducing the greenhouse gas emissions of summer maize in intensive agricultural systems. However, the trade-off between the economic and environmental performances of different blended fertilizer treatments for different maize varieties remains unclear. Therefore, a consecutive two-year field experiment was conducted in the North China Plain to study the effects of different ratios of CRU and common urea on the yield, nitrous oxide (N2O) emissions, yield-scaled total N2O emissions, greenhouse gas intensity (GHGI), and net ecosystem economic benefit (NEEB) in 2021 and 2022. Four N fertilizer treatments with equal rate at 180 kg N ha-1 were applied as N180U (all Urea), N180C1(1/3CRU), N180C2(2/3CRU), and N180C (all CRU), and two maize varieties (JNK728-yellow ripe variety and ZD958-green ripe variety) were used. The N180C1 and N180C2 treatments produced the highest grain yield in varieties JNK728 and ZD958 (9.4-11.5 t ha-1 and 9.0-11.0 t ha-1), respectively. Compared to the N180U treatment (conventional method), the N180C1 treatment reduced the GHGI (24.8 %-25.9 %) and increased the NEEB (33.1 %-33.4 %) in the JNK728 variety, whereas the N180C2 treatment reduced the GHGI (16.9 %-28.8 %) and increased the NEEB (27.2 %-48.1 %) in the ZD958 variety. The study concludes that a one-time application of blended nitrogen fertilizer in suitable varieties can minimize the GHGI and maximize the NEEB, which is an effective strategy for balancing yield and nitrogen efficiency in the summer maize system in the North China Plain.

High-throughput assays to identify archaea-targeting nitrification inhibitors

Nitrification is a microbial process that converts ammonia (NH3) to nitrite (NO2 -) and then to nitrate (NO3 -). The first and rate-limiting step in nitrification is ammonia oxidation, which is conducted by both bacteria and archaea. In agriculture, it is important to control this process as high nitrification rates result in NO3 - leaching, reduced nitrogen (N) availability for the plants and environmental problems such as eutrophication and greenhouse gas emissions. Nitrification inhibitors can be used to block nitrification, and as such reduce N pollution and improve fertilizer use efficiency (FUE) in agriculture. Currently applied inhibitors target the bacteria, and do not block nitrification by ammonia-oxidizing archaea (AOA). While it was long believed that nitrification in agroecosystems was primarily driven by bacteria, recent research has unveiled potential significant contributions from ammonia-oxidizing archaea (AOA), especially when bacterial activity is inhibited. Hence, there is also a need for AOA-targeting nitrification inhibitors. However, to date, almost no AOA-targeting inhibitors are described. Furthermore, AOA are difficult to handle, hindering their use to test or identify possible AOA-targeting nitrification inhibitors. To address the need for AOA-targeting nitrification inhibitors, we developed two miniaturized nitrification inhibition assays using an AOA-enriched nitrifying community or the AOA Nitrosospaera viennensis. These assays enable high-throughput testing of candidate AOA inhibitors. We here present detailed guidelines on the protocols and illustrate their use with some examples. We believe that these assays can contribute to the discovery of future AOA-targeting nitrification inhibitors, which could complement the currently applied inhibitors to increase nitrification inhibition efficiency in the field and as such contribute to a more sustainable agriculture.

Nitrogen fertilization application strategies improve yield of the rice cultivars with different yield types by regulating phytohormones

Rice (Oryza sativa L.) is the most important food crop worldwide, and its sustainable development is essential to ensure global food security. Panicle morphological and physiological characteristics plays an important role in rice yield formation. However, under different nitrogen (N) fertilization strategies, it is not clear whether the morphological and physiological state of panicles at panicle development stage affects the formation of yield. To understand how the panicle differentiation and development, and grain yield are affected by the N fertilization strategies, and clarify the relationship between related traits and yield in the process of panicle development in different cultivars. In this study consisted of no N fertilizer and four N fertilization strategies, a panicle weight type (PWT) rice cultivar, Dongfu 114 (DF114) and a panicle number type (PNT) rice cultivar, Longdao 11 (LD11) were grown in the field. The results showed that N fertilization strategies could improve the nitrogen use efficiency and yield of rice, but the response of different rice varieties to N fertilizer strategies was different. Different from the DF114, the further increase of panicle N fertilizer ratio could not further improve the yield of LD11, and the highest grain yield of DF114 and LD11 was obtained under N4 and N3 conditions, respectively. In addition, this study found that N fertilizer strategies can affect the content of phytohormones in rice at the panicle differentiation stage, and then regulate the differentiation and development of rice panicles to affect yield. It is of great significance to optimize the application mode of N fertilizer according to the characteristics of varieties to improve rice yield and ensure food security.

Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains

IMPORTANCE

Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.

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.

Genetic variation among elite inbred lines suggests potential to breed for BNI-capacity in maize

Biological nitrification inhibition (BNI) is a plant function where root systems release antibiotic compounds (BNIs) specifically aimed at suppressing nitrifiers to limit soil-nitrate formation in the root zone. Little is known about BNI-activity in maize (Zea mays L.), the most important food, feed, and energy crop. Two categories of BNIs are released from maize roots; hydrophobic and hydrophilic BNIs, that determine BNI-capacity in root systems. Zeanone is a recently discovered hydrophobic compound with BNI-activity, released from maize roots. The objectives of this study were to understand/quantify the relationship between zeanone activity and hydrophobic BNI-capacity. We assessed genetic variability among 250 CIMMYT maize lines (CMLs) characterized for hydrophobic BNI-capacity and zeanone activity, towards developing genetic markers linked to this trait in maize. CMLs with high BNI-capacity and ability to release zeanone from roots were identified. GWAS was performed using 27,085 SNPs (with unique positions on the B73v.4 reference genome, and false discovery rate = 10), and phenotypic information for BNI-capacity and zeanone production from root systems. Eighteen significant markers were identified; three associated with specific BNI-activity (SBNI), four with BNI-activity per plant (BNIPP), another ten were common between SBNI and BNIPP, and one with zeanone release. Further, 30 annotated genes were associated with the significant SNPs; most of these genes are involved in pathways of "biological process", and one (AMT5) in ammonium regulation in maize roots. Although the inbred lines in this study were not developed for BNI-traits, the identification of markers associated with BNI-capacity suggests the possibility of using these genomic tools in marker-assisted selection to improve hydrophobic BNI-capacity in maize.

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.

Characterization of yield and cumulative nitrous oxide emission of maize varieties in responses to different nitrogen application rates

The nitrogen use efficiency (NUE) of maize is usually below 60%. Considering future food supply and climate change, selective breeding of maize with high nitrogen (N)-efficient varieties, covering genetic diversities, is an effective strategy for identifying specific elements for controlling NUE and productivity per arable farming unit while reducing environmental damage. This study evaluated the yield and nitrous oxide (N₂O) emission of 30 maize varieties under two different N doses of 57.5 kg N ha^-1 (N1, N-sufficient) and 173 kg N ha^-1 (N3, N-high) applied in two equal splits on 2 and 4 weeks after germination (WAG). Then, the tested maize varieties were categorized into four groups based on the grain yield and cumulative N₂O, that is, efficient-efficient (EE) under both N1 and N3, high-N efficient (HNE) under N3 only, low-N efficient (LNE) under N1 only, and nonefficient-nonefficient (NN) under neither N1 nor N3. Maize yield was significantly positively correlated with shoot biomass, N-accumulation, and kernel-number under N1 and with N₂O-flux at 5 WAG, NH₄⁺, shoot biomass, and all of yield components under N3, whereas cumulative N₂O showed a significant positive correlation with NO₃^- under N3 only and with N₂O flux at 3 WAG under both N levels. The EE generally showed higher grain yield, yield components, N-accumulation, dry matter accumulation, root volume, and NH₄⁺ in soil and lower cumulative N₂O and NO₃^- in soil relative to NN maize varieties. The EE variety groups of maize can be a feasible strategy for increasing N fertilizer efficiency without reducing maize production as well as decrease the negative impact of N lost in agricultural system.

Benefits of biological nitrification inhibition of Leymus chinensis under alkaline stress: the regulatory function of ammonium-N exceeds its nutritional function

Introduction

The production of root exudates with biological nitrification inhibition (BNI) effects is a strategy adopted by ammonium-N (NH4+-N) tolerant plant species that occur in N-limited environments. Most knowledge on BNI comes from plant species that occur in acidic soils.

Methods

Here, combining field sampling and laboratory culture, we assessed the BNI-capacity of Leymus chinensis, a dominant grass species in alkaline grasslands in eastern Asia, and explored why L. chinensis has BNI ability.

Results and discussion

The results showed that L. chinensis has strong BNI-capacity. At a concentration of 1 mg mL^-1, L. chinensis' root exudates inhibited nitrification in soils influenced by Puccinellia tenuiflora by 72.44%, while DCD only inhibited it by 68.29%. The nitrification potential of the soil of L. chinensis community was only 53% of the P. tenuiflora or 41% of the Suaeda salsa community. We also showed that the supply of NH4+-N driven by L. chinensis' BNI can meet its requirements . In addition, NH4+-N can enhance plant adaptation to alkaline stress by regulating pH, and in turn, the uptake of nitrate-N (NO3--N). We further demonstrated that the regulatory function of NH4+-N is greater than its nutritional function in alkaline environment. The results offer novel insights into how L. chinensis adapts to high pH and nutrient deficiency stress by secreting BNIs, and reveal, for the first time, differences in the functional roles of NH4+-N and NO3--N in growth and adaptation under alkaline conditions in a grass species.

An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition activity

Several plant species have been reported to inhibit nitrification via their root exudates, the so-called biological nitrification inhibition (BNI). Given the potential of BNI-producing plants to sustainably mitigate N losses in agrosystems, identification of BNI activity in existing germplasms is of paramount importance. A hydroponic system was combined with an optimized Nitrosomonas europaea-based bioassay to determine the BNI activity of root exudates. The pipeline allows collecting and processing hundreds of root exudates simultaneously. An additional assay was established to assess the potential bactericide effect of the root exudates. The pipeline was used to unravel the impact of developmental stage, temperature and osmotic stress on the BNI trait in selected wheat genotypes. Biological nitrification inhibition activity appeared consistently higher in wheat at the pretillering stage as compared to the tillering stage. While low-temperatures did not alter BNI activities in root exudates, osmotic stress appeared to change the BNI activity in a genotype-dependent manner. Further analysis of Nitrosomonas culture after pre-exposure to root exudates suggested that BNI activity has no or limited bactericide effects. The present pipeline will be instrumental to further investigating the dynamics of BNI activity and to uncover the diversity of the BNI trait in plant species.

Influence of biochar-based urea substituting urea on rice yield, bacterial community and nitrogen cycling in paddy fields

BACKGROUND

There is an increasing understanding of the importance of biochar-based fertilizers in agroecosystems. However, no research has evaluated the effects of partial substitution of urea with biochar-based urea on rice yields and soil microbial communities. We therefore investigated the rice yields, bacterial communities, and gene abundance involved in nitrogen in silty clay and sandy loam soil paddy fields treated with urea (U), total substitution of urea with biochar-based urea (BSU), partial substitution of urea with biochar-based urea in basal and tillering fertilizers (BSU1), and partial substitution of urea with biochar-based urea in panicle fertilizers (BSU2).

RESULTS

Compared with U, applying biochar-based urea increased rice yields, with BSU2 having the most notable effect. Principal coordinate analysis revealed that bacterial communities treated with BSU2 in both soils were significantly different from those treated with U and BSU, most probably due to the decrease in pH caused by the decrease in the concentration of ammonium. The relative abundance of Subdivision3_genera_incertae_sedis, Azotobacter, Geobacter, Buchnera, and Terrimonas in silty clay soils and Saccharibacteria_genera_incertae_sedis and Geobacter in sandy loam soils significantly increased when treated with BSU2 and was positively correlated with rice yields, indicating that the improvements in rice yield were associated with changes in bacterial communities. Based upon amoA/narG related to nitrate accumulation and norB/nosZ related to nitrous oxide emissions, BSU2 enabled a lower risk of nitrate leaching and nitrous oxide emissions in both soils, in comparison with the U and BSU treatments.

CONCLUSION

The BSU2 treatment had a stronger yield-increasing effect than biochar-based urea alone and lowered the risk of nitrogen pollution, which is beneficial to the sustainable development of paddy fields. © 2022 Society of Chemical Industry.

Non-native Brachiaria humidicola with biological nitrification inhibition capacity stimulates in situ grassland N2O emissions

Introduction

Brachiaria humidicola, a tropical grass, could release root exudates with biological nitrification inhibition (BNI) capacity and reduce soil nitrous oxide (N2O) emissions from grasslands. However, evidence of the reduction effect in situ in tropical grasslands in China is lacking.

Methods

To evaluate the potential effects of B. humidicola on soil N2O emissions, a 2-year (2015–2017) field experiment was established in a Latosol and included eight treatments, consisting of two pastures, non-native B. humidicola and a native grass, Eremochloa ophiuroide, with four nitrogen (N) application rates. The annual urea application rates were 0, 150, 300, and 450 kg N ha−1.

Results

The average 2-year E. ophiuroides biomass with and without N fertilization were 9.07–11.45 and 7.34 t ha−1, respectively, and corresponding values for B. humidicola increased to 31.97–39.07 and 29.54 t ha−1, respectively. The N-use efficiencies under E. ophiuroide and B. humidicola cultivation were 9.3–12.0 and 35.5–39.4%, respectively. Annual N2O emissions in the E. ophiuroides and B. humidicola fields were 1.37 and 2.83 kg N2O-N ha−1, respectively, under no N fertilization, and 1.54–3.46 and 4.30–7.19 kg N2O-N ha−1, respectively, under N fertilization.

Discussions

According to the results, B. humidicola cultivation increased soil N2O emissions, especially under N fertilization. This is because B. humidicola exhibited the more effective stimulation effect on N2O production via denitrification primarily due to increased soil organic carbon and exudates than the inhibition effect on N2O production via autotrophic nitrification. Annual yield-scaled N2O emissions in the B. humidicola treatment were 93.02–183.12 mg N2O-N kg−1 biomass, which were significantly lower than those in the E. ophiuroides treatment. Overall, our results suggest that cultivation of the non-native grass, B. humidicola with BNI capacity, increased soil N2O emissions, while decreasing yield-scaled N2O emissions, when compared with native grass cultivation.

Role of mycorrhizas and root exudates in plant uptake of soil nutrients (calcium, iron, magnesium, and potassium): has the puzzle been completely solved?

Anthropogenic global change is driving an increase in the frequency and intensity of drought and flood events, along with associated imbalances and limitation of several soil nutrients. In the context of an increasing human population, these impacts represent a global-scale challenge for biodiversity conservation and sustainable crop production to ensure food security. Plants have evolved strategies to enhance uptake of soil nutrients under environmental stress conditions; for example, symbioses with fungi (mycorrhization) in the rhizosphere and the release of exudates from roots. Although crop cultivation is managed for the effects of limited availability of nitrogen (N) and phosphorus (P), there is increasing evidence for limitation of plant growth and fitness because of the low availability of other soil nutrients such as the metals potassium (K), calcium (Ca), magnesium (Mg), and iron (Fe), which may become increasingly limiting for plant productivity under global change. The roles of mycorrhizas and plant exudates on N and P uptake have been studied intensively; however, our understanding of the effects on metal nutrients is less clear and still inconsistent. Here, we review the literature on the role of mycorrhizas and root exudates in plant uptake of key nutrients (N, P, K, Ca, Mg, and Fe) in the context of potential nutrient deficiencies in crop and non-crop terrestrial ecosystems, and identify knowledge gaps for future research to improve nutrient-uptake capacity in food crop plants.

PANOMICS at the interface of root-soil microbiome and BNI

Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N₂O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.

The nitrification inhibitor 1,9-decanediol from rice roots promotes root growth in Arabidopsis through involvement of ABA and PIN2-mediated auxin signaling

1,9-decanediol (1,9-D) is a biological nitrification inhibitor secreted in roots, which effectively inhibits soil nitrifier activity and reduces nitrogen loss from agricultural fields. However, the effects of 1,9-D on plant root growth and the involvement of signaling pathways in the plant response to 1,9-D have not been investigated. Here, we report that 1,9-D, in the 100-400 μM concentration range, promotes primary root length in Arabidopsis seedlings at 3d and 5d, by 10.1%-33.3% and 6.9%-32.6%, and, in a range of 50-200 μM, leads to an increase in the number of lateral roots. 150 μM 1,9-D was found optimum for the positive regulation of root growth. qRT-PCR analysis reveals that 1,9-D can significantly increase AtABA3 gene expression and that a mutation in ABA3 results in insensitivity of root growth to 1,9-D. Moreover, through pharmacological experiments, we show that exogenous addition of ABA (abscisic acid) with 1,9-D enhances primary root length by 23.5%-63.3%, and an exogenous supply of 1,9-D with the ABA inhibitor Flu reduces primary root length by 1.0%-14.3%. Primary root length of the pin2/eir1-1 is shown to be insensitive to both exogenous addition of 1,9-D and ABA, indicating that the auxin carrier PIN2/EIR1 is involved in promotion of root growth by 1,9-D. These results suggest a novel for 1,9-D in regulating plant root growth through ABA and auxin signaling.

Syringic acid from rice roots inhibits soil nitrification and N2O emission under red and paddy soils but not a calcareous soil

Syringic acid (SA) is a novel biological nitrification inhibitor (BNIs) discovered in rice root exudates with significant inhibition of Nitrosomonas strains. However, the inhibitory effect of SA on nitrification and nitrous oxide (N₂O) emissions in different soils and the environmental factors controlling the degree of inhibition have not been studied. Using 14-day microcosm incubation, we investigated the effects of different concentrations of SA on nitrification activity, abundance of ammonia-oxidizing microorganisms, and N₂O emissions in three typical agricultural soils. The nitrification inhibitory efficacy of SA was strongest in acidic red soil, followed by weakly acidic paddy soil, with no significant effect in an alkaline calcareous soil. Potential nitrification activity (PNA) were also greatly reduced by SA additions in paddy and red soil. Pearson correlation analysis showed that the inhibitory efficacy of SA might be negatively correlated with soil pH and positively correlated with clay percentage. SA treatments significantly reduced N₂O emissions by 69.1-79.3% from paddy soil and by 40.8%-46.4% from red soil, respectively, but no effect was recorded in the calcareous soil. SA addition possessed dual inhibition of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance in paddy and red soil. Structural equation modelling revealed that soil ammonium (NH₄ ⁺) and dissolved organic carbon content (DOC) were the key variables explaining AOA and AOB abundance and subsequent N₂O emissions. Our results support the potential for the use of the BNI SA in mitigating N₂O emissions and enhancing N utilization in red and paddy soils.

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.

Effect of microbial community structures and metabolite profile on greenhouse gas emissions in rice varieties

Rice paddy fields are major sources of atmospheric methane (CH₄) and nitrous oxide (N₂O). Rice variety is an important factor affecting CH₄ and N₂O emissions. However, the interactive effects of rice metabolites and microorganisms on CH₄ and N₂O emissions in paddy fields are not clearly understood. In this study, a high greenhouse gas-emitting cultivar (YL 6) and a low greenhouse gas-emitting cultivar (YY 1540) were used as experimental materials. Metabolomics was used to examine the roots, root exudates, and bulk soil metabolites. High-throughput sequencing was used to determine the microbial community composition. YY 1540 had more secondary metabolites (flavonoids and isoflavonoids) in root exudates than YL 6. It was enriched with the uncultured members of the families Gemmatimonadanceae and Rhizobiales_Incertae_Sedis in bulk soil, and genera Burkholderia-Caballeronia-Paraburkholderia, Magnetospirillum, Aeromonas, and Anaeromyxobacter in roots, contributing to increased expression of pmoA and nosZ genes and reducing CH₄ and N₂O emissions. YL 6 roots and root exudates contained higher contents of carbohydrates [e.g., 6-O- acetylarbutin and 2-(3- hydroxyphenyl) ethanol 1'-glucoside] than those of YY 1540. They were enriched with genera RBG-16-58-14 in bulk soil and Exiguobacterium, and uncultured member of the Kineosporiaceae family in roots, which contributed to increased expression of mcrA, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nirS, and nirK genes and greenhouse gas emissions. In general, these results established a link between metabolites, microorganisms, microbial functional genes, and greenhouse gas emissions. The metabolites of root exudates and roots regulated CH₄ and N₂O emissions by influencing the microbial community composition in bulk soil and roots.

The rice transcription factor Nhd1 regulates root growth and nitrogen uptake by activating nitrogen transporters

Plants adjust root architecture and nitrogen (N) transporter activity to meet the variable N demand, but their integrated regulatory mechanism remains unclear. We have previously reported that a floral factor in rice (Oryza sativa), N-mediated heading date-1 (Nhd1), regulates flowering time. Here, we show that Nhd1 can directly activate the transcription of the high-affinity ammonium (NH4+) transporter 1;3 (OsAMT1;3) and the dual affinity nitrate (NO3-) transporter 2.4 (OsNRT2.4). Knockout of Nhd1 inhibited root growth in the presence of NO3- or a low concentration of NH4+. Compared to the wild-type (WT), nhd1 and osamt1;3 mutants showed a similar decrease in root growth and N uptake under low NH4+ supply, while nhd1 and osnrt2.4 mutants showed comparable root inhibition and altered NO3- translocation in shoots. The defects of nhd1 mutants in NH4+ uptake and root growth response to various N supplies were restored by overexpression of OsAMT1;3 or OsNRT2.4. However, when grown in a paddy field with low N availability, nhd1 mutants accumulated more N and achieved a higher N uptake efficiency (NUpE) due to the delayed flowering time and prolonged growth period. Our findings reveal a molecular mechanism underlying the growth duration-dependent NUpE.

Harnessing belowground processes for sustainable intensification of agricultural systems

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.

Foliar-applied cerium oxide nanomaterials improve maize yield under salinity stress: Reactive oxygen species homeostasis and rhizobacteria regulation

Salinity stress seriously threatens agricultural productivity and food security worldwide. This work reports on the mechanisms of alleviating salinity stress by cerium oxide nanomaterials (CeO2 NMs) in maize (Zea may L.). Soil-grown maize plants were irrigated with deionized water or 100 mM NaCl solution as the control or the salinity stress treatment. CeO2 NMs (1, 5, 10, 20, and 50 mg/L) with antioxidative enzyme mimicking activities were foliarly applied on maize leaves for 7 days. The morphological, physiological, biochemical, and transcriptomic responses of maize were evaluated. Specifically, salinity stress significantly reduced 59.0% and 63.8% in maize fresh and dry biomass, respectively. CeO₂ NMs at 10, 20, and 50 mg/L improved the salt tolerance of maize by 69.5%, 69.1%, and 86.8%, respectively. Also, 10 mg/L CeO₂ NMs maintained Na⁺/K⁺ homeostasis, enhanced photosynthetic efficiency by 30.8%, and decreased reactive oxygen species (ROS) level by 58.5% in salt-stressed maize leaves. Transcriptomic analysis revealed that the antioxidative defense system-related genes recovered to the normal control level after CeO₂ NMs application, indicating that CeO₂ NMs eliminated ROS through their intrinsic antioxidative enzyme properties. The down-regulation of genes related to lignin synthesis in the phenylpropanoid biosynthesis pathway accelerated leaf cell elongation. In addition, CeO₂ NMs increased the rhizobacteria richness and diversity through the increment of carbon source in root exudates and improved the abundance of halotolerant plant growth-promoting rhizobacteria (HT-PGPR). Importantly, the yield of salt-stressed maize was enhanced by 293.3% after 10 mg/L CeO₂ NMs foliar application. These results will provide new insights for the application of CeO₂ NMs in management to reduce the salinity-caused crop loss.

Diversity of rice rhizosphere microorganisms under different fertilization modes of slow-release fertilizer

The application of slow-release fertilizer is an effective way to satisfy the demand for nutrients of crops. The objective of present study was to investigate the microbial community characteristics in rice rhizosphere soil under different fertilization modes of slow-release fertilizer. Three fertilization modes of slow-release fertilizer, i.e., (CK) manually broadcasted on the soil surface at 300 kg·ha⁻¹ before transplanting and then same fertilizer rate was applied at the same way one week after transplanting; (SF) 10 cm depth mechanized placement at 600 kg·ha⁻¹ during the transplanting; (DSF) 10 cm depth mechanized placement at 480 kg·ha⁻¹ during the transplanting, were adopt in the field experiment. The results showed that SF and DSF treatments promoted richness (ACE and Chao1 values) and diversity (Shannon value) of rice rhizosphere microorganisms compared with CK treatment. Compared with CK, SF treatment increased relative abundances of Planctomycetes and decreased relative abundance of Nitrospirae, DSF treatments increased relative abundances of Deltaproteobacteria. Moreover, higher relative abundances of Paenibacillus and Sphingomonas were recorded in DSF treatment than CK. In addition, the partial factor productivity (PFP) deep placement of slow-release fertilizer treatment was significantly higher than that of CK treatment. DSF treatment increased the yield by 16.61% compared with CK treatment while reducing fertilizer input by 20%. In conclusion, compared with broadcasting, deep placement of slow-release fertilizer could improve the structure, distribution, and diversity of the microbial community in rice rhizosphere soil, and increase the utilization rate of fertilizers, and increase rice yield.

Whole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiency

Nutrient use efficiency (NUE) is typically measured as the ratio of yield to soil nutrient availability but ignores contributions of underlying plant traits. Relevant plant traits can be grouped as root acquisition efficiency, shoot radiation use efficiency, and plant metabolic efficiency. The intentional integration of these traits will lead to synergistic improvements of NUE. Recent progress in trait-focused research includes phenotyping root nutrient uptake rates and respiration, engineering reduced photorespiration, and identification of nutrient assimilation pathways. Traits need to be conceptualized in agricultural systems contexts to improve synchrony of plant demand and soil supply of nutrients, including consideration of crop mixtures. Use of simulation modeling and multi-objective optimization will allow accelerating NUE gains beyond selection for a single ratio.

Root exudates impact plant performance under abiotic stress

Plant root exudates serve pivotal roles in supporting plant development and interactions with the physicochemical and biological factors in the rhizosphere. Under stress conditions, root exudation is involved in enhancing plant resource-use efficiency and facilitating the crosstalk between plant and soil microbes to ameliorate stress. Although there are a large number of root exudates that remain to be characterized, recent technological advancements have allowed for the function of many exudate compounds to be elucidated. In this review, we discuss current knowledge about the key root exudates that modulate plant resource-use efficiency under various abiotic stresses including drought, aluminum toxicity, phosphorus, nitrogen, and iron deficiency. The role that key root exudates play in shaping microbial communities in the rhizosphere under stress conditions is also an important consideration addressed in this review.

Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers

The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH₄ ⁺-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N₂ production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH₄ ⁺, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.

Root exudation of contrasting drought-stressed pearl millet genotypes conveys varying biological nitrification inhibition (BNI) activity

Roots secrete a vast array of low molecular weight compounds into the soil broadly referred to as root exudates. It is a key mechanism by which plants and soil microbes interact in the rhizosphere. The effect of drought stress on the exudation process and composition is rarely studied, especially in cereal crops. This study focuses on comparative metabolic profiling of the exudates from sensitive and tolerant genotypes of pearl millet after a period of drought stress. We employed a combined platform of gas and liquid chromatography coupled to mass spectrometry to cover both primary and secondary metabolites. The results obtained demonstrate that both genotype and drought stress have a significant impact on the concentration and composition of root exudates. The complexity and function of these differential root exudates are discussed. To reveal the potential effect of root exudates on the soil microbial community after a period of drought stress, we also tested for biological nitrification inhibition (BNI) activity. The analysis revealed a genotype-dependent enhancement of BNI activity after a defined period of drought stress. In parallel, we observed a genotype-specific relation of elongated root growth and root exudation under drought stress. These data suggest that the drought stress-dependent change in root exudation can manipulate the microbial soil communities to adapt and survive under harsh conditions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00374-021-01578-w.

Improved Nitrogen Use Efficiency and Greenhouse Gas Emissions in Agricultural Soils as Producers of Biological Nitrification Inhibitors

Based on an analysis of the current situation of nitrogen fertiliser application, it is suggested that improving the nitrogen utilisation efficiency of crops is an important means of promoting the sustainable development of agriculture and realises the zero increase in chemical fertiliser application. Nitrate loss and nitrous oxide (N₂O) emissions caused by nitrification and denitrification are the main reasons for the low utilisation rate of nitrogen fertilisers. N₂O is a greenhouse gas that has caused a sharp increase in global temperature. Biological nitrification inhibition refers to releasing natural compounds that inhibit nitrification from plant roots. The natural compounds released are called biological nitrification inhibitors (BNIs), which specifically inhibit the activity of microorganisms in soil nitrification. Biological nitrification inhibitors can significantly improve rice (Oryza sativa), corn (Zea mays) and other crops by 5-10%, which can increase the nitrogen utilisation rate of corn by 3.1%, and reduce greenhouse gas N₂O emissions. Compared with plants that do not produce BNI, the amount of N₂O released can be reduced by up to 90%. The BNI released by Brachialactone (Brachiaria humidicola) accounted for 60-90% of the total inhibition of nitrification. In summary, biological nitrification inhibitors that inhibit nitrification, improve nitrogen utilisation and crop yield, and reduce greenhouse gas emissions play an important role. This paper reviews the plants known to release BNIs, reviews the plants known to inhibit soil nitrification but with unknown BNIs and further discusses the important role of bio nitrification inhibition in agricultural systems.

Coordination of nitrogen uptake and assimilation favours the growth and competitiveness of moso bamboo over native tree species in high-NH4+ environments

Phenotypic plasticity and competitive strength are major mechanisms determining the success of invasive species and are influenced by abiotic factors. A rise in the ratio of ammonium (NH₄⁺) to nitrate (NO₃^-) in soils is frequently associated with the invasion of bamboo into broad-leaved evergreen forests. However, the influence of soil nitrogen (N) chemistry on plant growth and interspecific competition in the context of invasion remains insufficiently studied. In the present work, differences in plasticity and interspecific competition between native tree species in broad-leaved evergreen forests and invasive bamboo in response to different N forms were investigated using seedlings grown in a controlled environment. We show that moso bamboo responded positively and strongly to increased soil NH₄⁺/NO₃^- ratios, while the native tree species Sapium sebiferum, Camellia oleifera, and Machilus pauhoi responded negatively and exhibited limited plasticity. Native tree species growth was significantly inhibited in the presence of moso bamboo under high-NH₄⁺ conditions, whereas native tree species were less affected by interspecific competition when NO₃^- was supplied as the sole N source. By contrast, moso bamboo growth was significantly inhibited, followed by seedling death, in both monoculture and in mixed culture with prolonged NO₃^- treatment. All species tested exhibited significantly higher rates of ¹⁵NH₄⁺ than ¹⁵NO₃^- uptake, but the Michaelis constant (K_m) for ¹⁵NH₄⁺ uptake was lower in moso bamboo, indicating higher substrate affinity. Nitrate reductase (NR) and nitrite reductase (NiR) activities showed no inducible effects in moso bamboo compared to the induction response seen in the native tree species in response to NO₃^-. Activities of glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH) significantly increased with NH₄⁺ provision in roots of moso bamboo, contrasted by a less plastic response in the native tree species. Enhanced ammonification and reduced nitrification in soils is typically observed during bamboo invasion and appears to create a positive soil-plant feedback loop that, due to highly flexible and opportunistic NH₄⁺-acquisition pathways, favours bamboo fitness and invasion into native forests when NH₄⁺ is the dominant N form.

Impact of manure compost amendments on NH3 volatilization in rice paddy ecosystems during cultivation

Livestock manure has been widely used in agriculture to improve soil productivity and quality. However, intensive application can significantly enhance soil nitrogen (N) availability and facilitate ammonia (NH₃) volatilization during rice cultivation. The effects of different rates of manure application on the NH₃ volatilization rate, its mechanism, and their relationships have not been comprehensively investigated. In this study, field trials were conducted to investigate NH₃ volatilization in rice paddy soils amended with different livestock manure, cattle manure (CM), and swine manure (SM), at a rate of 0 (NPK), 10, 20, and 40 Mg ha^-1 during cultivation. Moreover, the soil physicochemical and biological properties and rice N uptake were investigated. Ultra-fine particulate matter (PM_2.5) was measured quantitatively and qualitatively. Manure application significantly increased NH₃ emissions compared to the control. Much higher volatilization rates were observed in the SM soils than in the CM soils, even when the same amount of N was applied. This is mainly related to the higher labile NH₄⁺ concentration and urease activity in SM soils. With increasing application levels, NH₃ emission rates proportionally increased in the SM, but there was no significant difference in the CM. Livestock manure application significantly increased NH₃ volatilization, particularly during the initial manure application and additional fertilization stages during rice cultivation. The results showed that the application of livestock manure significantly increased NH₃ volatilization. Moreover, the biochemical properties of manure composts, including labile N and urease activity, mainly affected NH₃ dynamics in rice paddies during cultivation rather than their type. Irrespective of manure application, PM_2.5, did not show a significant difference at the initial stage of cultivation. NH₃ volatilization was not significantly correlated with the formation of PM_2.5. It is necessary to develop effective strategies for mitigating NH₃ volatilization and maintaining soil quality without decreasing rice productivity in paddy ecosystems.

Stigmasterol root exudation arising from Pseudomonas inoculation of the duckweed rhizosphere enhances nitrogen removal from polluted waters

Rhizospheric microorganisms such as denitrifying bacteria are able to affect 'rhizobioaugmention' in aquatic plants and can help boost wastewater purification by benefiting plant growth, but little is known about their effects on the production of plant root exudates, and how such exudates may affect microorganismal nitrogen removal. Here, we assess the effects of the rhizospheric Pseudomonas inoculant strain RWX31 on the root exudate profile of the duckweed Spirodela polyrrhiza, using gas chromatography/mass spectrometry. Compared to untreated plants, inoculation with RWX31 specifically induced the exudation of two sterols, stigmasterol and β-sitosterol. An authentic standard assay revealed that stigmasterol significantly promoted nitrogen removal and biofilm formation by the denitrifying bacterial strain RWX31, whereas β-sitosterol had no effect. Assays for denitrifying enzyme activity were conducted to show that stigmasterol stimulated nitrogen removal by targeting nitrite reductase in bacteria. Enhanced N removal from water by stigmasterol, and a synergistic stimulatory effect with RWX31, was observed in open duckweed cultivation systems. We suggest that this is linked to a modulation of community composition of nirS- and nirK-type denitrifying bacteria in the rhizosphere, with a higher abundance of Bosea, Rhizobium, and Brucella, and a lower abundance of Rubrivivax. Our findings provide important new insights into the interaction of duckweed with the rhizospheric bacterial strain RWX31 and their involvement in the aquatic N cycle and offer a new path toward more effective bio-formulations for the purification of N-polluted waters.

A review of root exudates and rhizosphere microbiome for crop production

Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.

Effects of biological nitrification inhibitors on nitrogen use efficiency and greenhouse gas emissions in agricultural soils: A review

To maintain and increase crop yields, large amounts of nitrogen fertilizers have been applied to farmland. However, the nitrogen use efficiency (NUE) of chemical fertilizer remains very low, which may lead to serious environmental problems, including nitrate pollution, air quality degradation and greenhouse gas (GHG) emissions. Nitrification inhibitors can alleviate nitrogen loss by inhibiting nitrification; thus, biological nitrification inhibition by plants has gradually attracted increasing attention due to its low cost and environmental friendliness. Research progress on BNI is reviewed in this article, including the source, mechanisms, influencing factors and application of BNIs. In addition, the impact of BNI on agriculture and GHG emissions is summarized from the perspective of agricultural production and environmental protection, and the key future research prospects of BNIs are also noted.

The Response of Grain Yield and Root Morphological and Physiological Traits to Nitrogen Levels in Paddy Rice

Rice (Oryza sativa L.) is an important crop in China. Although it is known that its yield is restricted by nitrogen (N) supply, the response of the root system to N supply specifically has not been systematically explored. This study aimed to investigate the effect of N uptake on grain yield to clarify the relationships between root morphophysiological traits and N uptake, and to understand relation between phytohormones and root morphophysiological traits. Two N-efficient absorption cultivars (NEAs) and two N-inefficient absorption cultivars (NIAs) were grown in the field, and three N conditions, deficient N (60 kg ha^-1), intermediate N (180 kg ha^-1), and sufficient N (240 kg ha^-1), were applied during the growing season. The results showed higher dry matter and grain yield in NEAs than in NIAs, which was mainly attributed to increased N uptake in the mid- and late growth stages under all N conditions. And NEAs have different root regulation methods to obtain higher N accumulation and yield under different N supply conditions. Under lower N conditions, compared with NIAs, NEAs shown greater total root length, root oxidation activity, and root active absorbing surface area and smaller root diameter owing to higher indole-3-acetic acid and cytokinin content and lower 1-aminocyclopropane-1-carboxylic acid content in the early growth stages to respond to low N stress faster, laying a morphophysiological basis for its high N-uptake capacity in the mid- and late growth stages. Under higher N conditions, NEAs had higher root oxidation activity and root active absorbing surface area for N uptake and yield formation owing to higher abscisic acid and cytokinin content in the mid- and late growth stages, which improved the seed setting rate, thereby increasing the rice grain yield. These results suggest that NEAs can optimize the morphophysiological characteristics of roots through phytohormone regulation to adapt to different nutrient conditions, thereby promoting N accumulation and yield formation in rice.

Rice recruits Sphingomonas strain HJY-rfp via root exudate regulation to increase chlorpyrifos tolerance and boost residual catabolism

Inoculation with pollution-degrading endophytes boosts the catabolism of residual contaminants and promotes the pollution adaptation of host plants. We investigated the interaction pattern between Sphingomonas strain HJY-rfp, a chlorpyrifos-degrading endophytic bacterium, and rice (Oryza sativa) under pesticide stress using hydroponic cultivation. We observed a notable trend of endophytic root colonization in rice plants treated with 10 mg l-1 chlorpyrifos solution, and after 24 h the migration of HJY-rfp enhanced the chlorpyrifos degradation rate in leaves and stems by 53.36% and 40.81%, respectively. Critically, the rice root exudate profile (organic acids and amino acids) changed under chlorpyrifos stress, and variations in the contents of several components affected the chemotactic behaviour of HJY-rfp. HJY-rfp colonization dramatically activated defensive enzymes, which enabled efficient scavenging of reactive oxygen species, and led to 9.8%, 22.5%, and 41.9% increases in shoot length, fresh weight, and accumulation of total chlorophyll, respectively, in rice suffering from oxidative damage by chlorpyrifos. Endophytic colonization caused up-regulation of detoxification genes that have shown a significant positive correlation with chlorpyrifos degradation in vivo. Collectively, our results demonstrate that agrochemical stress causes plants to actively recruit specific symbiotic microbes to detoxify contaminants and survive better under pollution conditions.

Rice Seedling Growth Promotion by Biochar Varies With Genotypes and Application Dosages

While biochar use in agriculture is widely advocated, how the effect of biochar on plant growth varies with biochar forms and crop genotypes is poorly addressed. The role of dissolvable organic matter (DOM) in plant growth has been increasingly addressed for crop production with biochar. In this study, a hydroponic culture of rice seedling growth of two cultivars was treated with bulk mass (DOM-containing), water extract (DOM only), and extracted residue (DOM-free) of maize residue biochar, at a volumetric dosage of 0.01, 0.05, and 0.1%, respectively. On seedling root growth of the two cultivars, bulk biochar exerted a generally negative effect, while the biochar extract had a consistently positive effect across the application dosages. Differently, the extracted biochar showed a contrasting effect between genotypes. In another hydroponic culture with Wuyunjing 7 treated with biochar extract at sequential dosages, seedling growth was promoted by 95% at 0.01% dosage but by 26% at 0.1% dosage, explained with the great promotion of secondary roots rather than of primary roots. Such effects were likely explained by low molecular weight organic acids and nanoparticles contained in the biochar DOM. This study highlights the importance of biochar DOM and crop genotype when evaluating the effect of biochar on plants. The use of low dosage of biochar DOM could help farmers to adopt biochar technology as a solution for agricultural sustainability.

Effects of cadmium on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings under elevated atmospheric CO2 scenarios

The individual impacts of elevated CO₂ and heavy metals on soil nitrification have been widely reported. However, studies on the combined effects of elevated CO₂ and heavy metals on soil nitrification are still limited. Here, a 135-day growth chamber experiment was conducted to investigate the impacts of elevated CO₂ and cadmium (Cd) levels on soil nitrification in the rhizosphere of Robinia pseudoacacia L. seedlings. Elevated CO₂ combined with Cd pollution generally stimulated ammonia monooxygenase (AMO), hydroxylamine oxidase (HAO), and nitrite oxidoreductase (NXR) activities. Compared to the control, the abundance of ammonia-oxidizing bacteria (AOB) at day 135 and ammonia-oxidizing archaea (AOA) increased significantly (p < 0.05) and the abundance of AOB at days 45 and 90 and that of the nitrite-oxidizing bacteria (NOB) decreased under elevated CO₂ + Cd. Elevated CO₂ mostly led to a significant (p < 0.05) decrease in soil nitrification intensity in the rhizosphere of R. pseudoacacia exposed to Cd. The effects of Cd, CO₂, and their interaction on HAO and NXR activities were significant (p < 0.01). Soil pH, the C/N ratio, water-soluble organic carbon, water-soluble organic nitrogen (WSON), and total carbon were the dominant factors (p < 0.05) affecting nitrifying enzyme activities and nitrification intensity in rhizosphere soils. Elevated CO₂ clearly affected AOA, AOB, and NOB community structures and dominant genera by shaping C/N ratio, pH, and Cd and WSON contents in rhizosphere soils under Cd exposure. Overall, the responses of pH, C/N ratio, WSON, and Cd to elevated CO₂ led to changes in rhizosphere soil nitrification under the combination of elevated CO₂ and Cd pollution.

A Research Road Map for Responsible Use of Agricultural Nitrogen

Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research opportunities in the areas of agronomy, plant breeding, biological N fixation (BNF), soil N cycling, and modeling to achieve responsible, sustainable use of N in agriculture. Amongst these opportunities, improved agricultural practices that synchronize crop N demand with soil N availability are low-hanging fruit. Crop breeding that targets root and shoot physiological processes will likely increase N uptake and utilization of soil N, while breeding for BNF effectiveness in legumes will enhance overall system NUE. Likewise, engineering of novel N-fixing symbioses in non-legumes could reduce the need for chemical fertilizers in agroecosystems but is a much longer-term goal. The use of simulation modeling to conceptualize the complex, interwoven processes that affect agroecosystem NUE, along with multi-objective optimization, will also accelerate NUE gains.

Rhizosphere pH and cation-anion balance determine the exudation of nitrification inhibitor 3-epi-brachialactone suggesting release via secondary transport

Biological nitrification inhibition (BNI) of Brachiaria humidicola has been attributed to nitrification-inhibiting fusicoccanes, most prominently 3-epi-brachialactone. However, its release mechanism from B. humidicola roots remains elusive. Two hydroponic experiments were performed to investigate the role of rhizosphere pH and nutritional N form in regulating 3-epi-brachialactone release by B. humidicola and verify the underlying release pathway. Low rhizosphere pH and NH₄ ⁺ nutrition promoted 3-epi-brachialactone exudation. However, the substitution of NH₄ ⁺ by K⁺ revealed that the NH₄ ⁺ effect was not founded in a direct physiological response to the N form but was related to the cation-anion balance during nutrient uptake. Release of 3-epi-brachialactone correlated with the transmembrane proton gradient ΔpH and NH₄ ⁺ uptake (R² = 0.92 for high ~6.8 and R² = 0.84 for low ~4.2 trap solution pH). This corroborated the release of 3-epi-brachialactone through secondary transport, with the proton motive force (ΔP) defining transport rates across the plasma membrane. It was concluded that 3-epi-brachialactone release cannot be conceptualized as a regulated response to soil pH or NH₄ ⁺ availability, but merely as the result of associated changes in ΔP.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Effect of perfluorooctanesulfonate (PFOS) on the rhizosphere soil nitrogen cycling of two riparian plants

Here, we examined the effects of low and high concentrations of perfluorooctanesulfonate (PFOS) on rhizosphere soil N cycling processes in the presence of Lythrum salicaria and Phragmites communis over 4 months. Compared with the control group, the nitrate nitrogen (NO₃^--N) content of the bulk soil in the low PFOS (0.1 mg kg^-1) treatment significantly decreased (27.7%), the ammonium nitrogen (NH₄⁺-N) content significantly increased (8.7%), and the pH value and total organic carbon (TOC) content slightly increased (0.3% and 1.1%, respectively). Compared with the low PFOS treatment, the content of NO₃^-N, NH₄⁺-N and pH value in the bulk soil of the high PFOS treatment (50 mg kg^-1) significantly increased (1.0%, 53.8% and 61.8%, respectively), and the TOC content significantly decreased (8.2%). Soil protease levels were high in the low PFOS treatment, but low in the high PFOS treatment. PFOS produced inverted U-shaped responses in the potential nitrification (1.5, 3.0, and 1.1 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), denitrification (0.19, 0.30, and 0.22 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), and N₂O emission rates (0.01, 0.03, and 0.02 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively) of bulk soil. The abundance of the archaea amoA gene decreased with increasing PFOS concentration, whereas that of bacterial amoA increased; inverted U-shaped responses were observed for narG, nirK, nirS, and nosZ. In the PFOS-contaminated rhizosphere soil, the observed changes differed from those in the bulk soil and differed between treatments. P. communis tended to upregulate each step of the nitrogen cycle under low PFOS conditions, whereas L. salicaria tended to inhibit them. Under high PFOS conditions, both test plants tended to act as inhibitors of the soil N-cycle; thus, the effects of PFOS on soil N transformation were plant-specific.

Rice nitrogen use efficiency does not link to ammonia volatilization in paddy fields

Ammonia (NH₃) volatilization is a major pathway of nitrogen (N) losses from paddy fields, and could be potentially mitigated by cultivation of high nitrogen use efficiency (high-NUE) rice cultivars. However, the relationship between NUE and NH₃ volatilization has not been validated under field conditions. A field experiment was conducted to evaluate the impact of four rice cultivars with different NUE [Wuyunjing 23 (W23), Zhendao 11 (Z11), Wuyujing 3 (W3), and Aoyusi 386 (A386)] on NH₃ volatilization, as well as the related mechanisms. Two high-NUE rice cultivars W23 and Z11 was not more effective in reducing total NH₃ volatilization from the paddy field compared to cultivar A386 with the lowest NUE. Cultivar A386 had 12.7-17.8% and 35.7-54.1% lower NH₃ volatilization than other three rice cultivars at tillering fertilization stage (TFS) and panicle fertilization stage (PFS), respectively, mainly due to its greater shoot N accumulation, root biomass and volume at TFS and its greater shoot biomass, leaf area index and shoot N accumulation at PFS. There was no significant difference in NH₃ volatilization among W23, Z11 and W3 at TFS. However, premature senescence phenomenon at later growth stages of A386 eventually led to its lowest NUE among the four rice cultivars. Our results suggest that NUE of rice does not link to NH₃ volatilization from paddy fields. In order to make high-NUE rice cultivars also effective in mitigating NH₃ volatilization, future breeding works should aim to improve N uptake capability and canopy structure at early tillering and panicle development stages while prevent premature senescence of rice plants to maintain high yields.