Micromanaging the nitrogen cycle in agroecosystems

Adaptive fluoride removal across concentration scales: Potential roles of microbial and acicular gypsum interactions in nitrogen and phosphate cycling

Fluoride contamination in groundwater is a critical environmental and public health concern. Traditional remediation methods, including chemical precipitation and adsorption, are hindered by low nucleation efficiency at low fluoride concentrations and severe microbial inhibition under high fluoride stress. This study introduces an adaptive two-stage remediation system that synergistically integrates abiotic and biotic mechanisms to achieve effective fluoride removal across concentration scales. In Stage I, under elevated fluoride stress (100 mg/L), acicular gypsum (AG) facilitated abiotic calcium precipitation, effectively reducing fluoride toxicity and creating favorable conditions for microbial activity. Residual calcium released from AG further supported microbial-induced calcium precipitation (MICP) in Stage II under lower fluoride stress (10 mg/L). The system achieved a fluoride removal efficiency of 98.85 % under high fluoride conditions and demonstrated consistent performance across a broad concentration range. This integrated approach, combining abiotic and biotic mechanisms, offers a promising strategy for addressing diverse fluoride contamination scenarios. Here, phosphate (P)-mediated mineralization and microbial denitrification drive pH modulation, stabilizing fluoride as fluorapatite [Ca5(PO4)3F]. Microbial community and network analysis revealed key taxa, including Cupriavidus and Ralstonia, which facilitated P cycling and fluorapatite formation. Additionally, Bradyrhizobium enhanced nitrogen (N) cycling and supported early microbial adaptation, emphasizing the interplay of microbial interactions in driving system functionality. Functional predictions using PICRUSt2 identified genes associated with N and P cycling, highlighting the capacity of the system for nutrient adaptation under complex environmental conditions.

Navigating nitrogen sustainability with microbiome-associated phenotypes

Crop microbiomes promote plant health through various mechanisms, including nutrient provisioning. However, agriculture neglected the importance of these microbiome-associated phenotypes (MAPs) in conventional management approaches originating from the Green Revolution. Green Revolution innovations, such as nitrogen fertilizers and high-yielding germplasm, supported an increase in global crop yields. Yet these advances also led to many environmental issues, including disruptions in microbially mediated nitrogen transformations that have reduced reliance on microbiomes for sustainable nitrogen acquisition. Overcoming the challenges introduced by the Green Revolution requires a shift toward ecologically informed agronomic strategies that incorporate MAPs into breeding and management decisions. Agriculture in the Anthropocene needs to mindfully manage crop microbiomes to decouple agrochemical inputs from profitable yields, minimizing the environmental repercussions of modern agriculture.

Microalgae and microbial inoculant as partial substitutes for chemical fertilizer enhance Polygala tenuifolia yield and quality by improving soil microorganisms

Excessive utilization of chemical fertilizers degrades the quality of medicinal plants and soil. Bio-organic fertilizers (BOFs) including microbial inoculants and microalgae have garnered considerable attention as potential substitutes for chemical fertilizer to enhance yield. In this study, a field experiment was conducted to investigate the effects of BOF partially substituting chemical fertilizer on the growth and quality of medicinal plant Polygala tenuifolia. The growth parameters, bioactive component contents, soil properties and composition of rhizosphere microorganisms were measured. The results indicated that substituting 40% of chemical fertilizer with microalgae showed the most pronounced growth-promoting effect, leading to a 29.30% increase in underground biomass and a 19.72% increase in 3,6'-disinapoylsucrose (DISS) content. Substituting 20% of chemical fertilizer with microalgae improved soil quality, significantly increasing soil organic matter content by 15.68% (p<0.05). Microalgae addition significantly affected the rhizosphere bacterial community composition of P. tenuifolia, reducing the relative abundance of Cladosporium by 33.33% and 57.93%, while increasing the relative abundance of Chloroflexi by 31.06% and 38.27%, under 20% and 40% chemical fertilizer reduction, respectively. The relative abundance of Chloroflexi positively correlated with both the underground biomass and DISS content (p<0.05), indicating that microalgae may stimulate Chloroflexi species associated with carbon cycling, thereby enhancing soil fertility, nutrient absorption, and ultimately leading to increased biomass accumulation and production of bioactive components in P. tenuifolia. In addition, there was no significant difference in underground growth and bioactive component contents between reduced chemical fertilizer dosage combined with solid microbial inoculant (SMI) and polyglutamic microbial inoculant (PMI), compared with 100% chemical fertilizer. Correlation analysis revealed that PMI could increase soil phosphorus availability through Streptomyces recruitment. In conclusion, our findings demonstrated that bio-organic fertilizers can partially substitute chemical fertilizer to improve soil properties and microorganisms, enhancing the growth and quality of P. tenuifolia. This provides a theoretical basis for increasing medicinal plant productivity under chemical fertilizer reduction.

The growing, resilient, inclusive and sustainable (GRINS) project for the development of life cycle inventory databases of beef cattle raised in Italy: The statistical datasets and the environmental assessment

Within the framework of the Growing, Resilient, Inclusive and Sustainable (GRINS) project (Spoke 1, WP3, Next Generation EU program), this work aims to overcome the absence of Italian beef cattle Life Cycle Inventory (LCI) datasets through a capillary analysis of several parameters. Specifically, the contribution to the environmental impact of livestock breeding of breed features (age, gender, weight, daily weight gain, breeding, feed intake and composition, milk and manure production), as well as stable management and crop cultivation was investigated. Statistical inventory datasets (84 in total) were developed for the predominant (<1 % population cut-off) beef cattle breeds in Italy. A key finding was the quantification of CH4 emissions from enteric fermentation (ranging from0.259 to 0.714 g kg-1 of live weight per day) and its contribution to the overall environmental impact of beef cattle breeding. The composition of feed rations emerged as critical, influencing both cattle emissions and environmental impacts associated with the cultivation and transport of raw materials. Intensive and langer breeds like Aubrac, Blond d'Aquitaine, Blue Belga, Charolaise, and Chianina, exhibited higher eco-indicator values compared to the extensive beef cattle breeds (Podolica, Highland, and Maremmana). The life cycle assessment identified several key impact categories (climate change, water use and ecotoxicity freshwater) mainly contributing to the total eco-indicator. Climate change (22.1 %) represented the greatest impact category, with beef cattle emissions over their lifespan averaging 9.3 Mg CO2-eq. Methane (enteric fermentation) and NH3 (manure management) emissions, as well as irrigation and pesticide use, represented the main hotspots. A comparative analysis evaluated the environmental footprint of Italian beef cattle against benchmarks outlined in the "Made Green in Italy" brand's Product Category Rules. This comparison revealed a 32.4 % reduction in total eco-indicator for Italian beef cattle, due to a significant decrease in freshwater ecotoxicity (-72.5 %), land use (-34.2) and climate change (-7.5 %).

The microbial-driven nitrogen cycle and its relevance for plant nutrition

Nitrogen (N) is a vital nutrient and an essential component of biological macromolecules such as nucleic acids and proteins. Microorganisms are major drivers of N-cycling processes in all ecosystems, including the soil and plant environment. The availability of N is a major growth-limiting factor for plants and it is significantly affected by the plant microbiome. Plants and microorganisms form complex interaction networks resulting in molecular signaling, nutrient exchange, and other distinct metabolic responses. In these networks, microbial partners influence growth and N use efficiency of plants either positively or negatively. Harnessing the beneficial effects of specific players within crop microbiomes is a promising strategy to counteract the emerging threats to human and planetary health due to the overuse of industrial N fertilizers. However, in addition to N-providing activities (e.g. the well-known symbiosis of legumes and Rhizobium spp.), other plant-microorganism interactions must be considered to obtain a complete picture of how microbial-driven N transformations might affect plant nutrition. For this, we review recent insights into the tight interplay between plants and N-cycling microorganisms, focusing on microbial N-transformation processes representing N sources and sinks that ultimately shape plant N acquisition.

Forage conservation is a neglected nitrous oxide source

Agricultural activities are the major anthropogenic source of nitrous oxide (N 2 O ), an important greenhouse gas and ozone-depleting substance. However, the role of forage conservation as a potential source ofN 2 O has rarely been studied. We investigatedN 2 O production from the simulated silage of the three major crops-maize, alfalfa, and sorghum-used for silage in the United States, which comprises over 90% of the total silage production. Our findings revealed that a substantialN 2 O could be generated, potentially placing forage conservation as the third largestN 2 O source in the agricultural sector. Notably, the application of chlorate as an additive significantly reducedN 2 O production, but neither acetylene nor intermittent exposure to oxygen showed any impact. Overall, the results highlight that denitrifiers, rather than nitrifiers, are responsible forN 2 O production from silage, which was confirmed by molecular analyses. Our study reveals a previously unexplored source ofN 2 O and provides a crucial mechanistic understanding for effective mitigation strategies.

Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere

Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.

Unlocking bacterial potential to reduce farmland N2O emissions

Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

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.

Emerging nitrogen-fixing cyanobacteria for sustainable cotton cultivation

Amid growing environmental concerns and the imperative for sustainable agricultural practices, this study examines the potential of nitrogen-fixing cyanobacteria as biofertilizers, particularly in cotton cultivation. The reliance on synthetic nitrogen fertilizers (SNFs), prevalent in modern agriculture, poses significant environmental challenges, including greenhouse gas emissions and water system contamination. This research aims to shift this paradigm by exploring the capacity of cyanobacteria as a natural and sustainable alternative. Utilizing advanced metabarcoding methods to analyze the 16S rRNA gene, we conducted a comprehensive assessment of soil bacterial communities within cotton fields. This study focused on evaluating the diversity, structure, taxonomic composition, and potential functional characteristics of these communities. Emphasis was placed on the isolation of native N2-fixing cyanobacteria strains rom cotton soils, and their subsequent effects on cotton growth. Results from our study demonstrate significant plant growth-promoting (PGP) activities, measured as N2 fixation, production of Phytohormones, Fe solubilization and biofertilization potential of five isolated cyanobacterial strains, underscoring their efficacy in cotton. These findings suggest a viable pathway for replacing chemical-synthetic nitrogen fertilizers with natural, organic alternatives. The reintegration of these beneficial species into agricultural ecosystems can enhance crop growth while fostering a balanced microbial environment, thus contributing to the broader goals of global sustainable agriculture.

Effects of two strains of thermophilic nitrogen-fixing bacteria on nitrogen loss mitigation in cow dung compost

Excavating nitrogen-fixing bacteria with high-temperature tolerance is essential for the efficient composting of animal dung. In this study, two strains of thermophilic nitrogen-fixing bacteria, NF1 (Bacillus subtilis) and NF2 (Azotobacter chroococcum), were added to cow dung compost both individually (NF1, NF2) and mixed together (NF3; mixing NF1 and NF2 at a ratio of 1:1). The results showed that NF1, NF2, and NF3 inoculants increased the total Kjeldahl nitrogen level by 38.43%-55.35%, prolonged the thermophilic period by 1-13 d, increased the seed germination index by 17.81%, and the emissions of NH3 and N2O were reduced by 25.11% and 42.75%, respectively. Microbial analysis showed that Firmicutes were the predominant bacteria at the thermophilic stage, whereas Chloroflexi, Proteobacteria, and Bacteroidetes were the predominant bacteria at the mature stage. These results confirmed that the addition of the isolated strains to cow dung composting improved the bacterial community structure and benefited nitrogen retention.

Nitrogen sensing and regulatory networks: it's about time and space

A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.

Nanoparticle applications in agriculture: overview and response of plant-associated microorganisms

Globally, food security has become a critical concern due to the rise in human population and the current climate change crisis. Usage of conventional agrochemicals to maximize crop yields has resulted in the degradation of fertile soil, environmental pollution as well as human and agroecosystem health risks. Nanotechnology in agriculture is a fast-emerging and new area of research explored to improve crop productivity and nutrient-use efficiency using nano-sized agrochemicals at lower doses than conventional agrochemicals. Nanoparticles in agriculture are applied as nanofertilizers and/or nanopesticides. Positive results have been observed in terms of plant growth when using nano-based agricultural amendments. However, their continuous application may have adverse effects on plant-associated rhizospheric and endospheric microorganisms which often play a crucial role in plant growth, nutrient uptake, and disease prevention. While research shows that the application of nanoparticles has the potential to improve plant growth and yield, their effect on the diversity and function of plant-associated microorganisms remains under-explored. This review provides an overview of plant-associated microorganisms and their functions. Additionally, it highlights the response of plant-associated microorganisms to nanoparticle application and provides insight into areas of research required to promote sustainable and precision agricultural practices that incorporate nanofertilizers and nanopesticides.

Intended and unintended impacts of nitrogen-fixing microorganisms and microbial inhibitors on nitrogen losses in contrasting maize cropping systems

Efforts to mitigate the nitrogen (N) footprint of maize production include using N-fixing microbes (NFM) and/or microbial inhibitors. We quantified the effects of NFM, the nitrification inhibitor (NI) 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture, and the urease inhibitor (UI) N-(n-butyl) thiophosphoric triamide, each applied by itself or paired with another additive, on nitrous oxide (N2 O) emissions, nitrate (NO3 - ) leaching, and crop performance in contrasting irrigated and rainfed maize systems over two growing seasons. We also used published emission factors to estimate indirect N2 O emissions from leached NO3 - that can be converted to N2 O. Agronomic effects were relatively small; the NI + NFM treatment increased N use efficiency and grain yield and protein content in some cases by 11%-14% relative to a treatment receiving only urea. Most of the additive treatments reduced direct (in-field) N2 O emissions, most consistently for treatments that contained NI which reduced emissions by 24%-77%. However, these beneficial effects were counteracted by increased NO3 - leaching, which occurred most consistently with UI or NFM applied as single additives or with NI. In these treatments, NO3 - leaching increased during at least one growing season, and at both sites, by factors of 2-7. In three site-years, increased NO3 - leaching with NFM and NI + NFM offset large reductions in direct N2 O, such that total direct + indirect N2 O emissions were not different from that in the urea only treatment. These unintended effects may have resulted from unfavorable rainfall timing, varying crop N demand, and declining additive effectiveness. Use of these soil additives requires caution and further study.

Feeding the world sustainably: efficient nitrogen use

Globally, overuse of nitrogen (N) fertilizers in croplands is causing severe environmental pollution. In this context, Gu et al. suggest environmentally friendly and cost-effective N management practices and Hamani et al. highlight the use of microbial inoculants to improve crop yields, while reducing N-associated environmental pollution and N-fertilizer use.

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

Ammonia Production Using Bacteria and Yeast toward a Sustainable Society

Ammonia is an important chemical that is widely used in fertilizer applications as well as in the steel, chemical, textile, and pharmaceutical industries, which has attracted attention as a potential fuel. Thus, approaches to achieve sustainable ammonia production have attracted considerable attention. In particular, biological approaches are important for achieving a sustainable society because they can produce ammonia under mild conditions with minimal environmental impact compared with chemical methods. For example, nitrogen fixation by nitrogenase in heterogeneous hosts and ammonia production from food waste using microorganisms have been developed. In addition, crop production using nitrogen-fixing bacteria has been considered as a potential approach to achieving a sustainable ammonia economy. This review describes previous research on biological ammonia production and provides insights into achieving a sustainable society.

Application of Stable Isotope Techniques in Tracing the Sources of Atmospheric NOX and Nitrate

Nitrate is an important component of PM2.5, and its dry deposition and wet deposition can have an impact on ecosystems. Nitrate in the atmosphere is mainly transformed by nitrogen oxides (NOX = NO + NO2) through a number of photochemical processes. For effective management of the atmosphere’s environment, it is crucial to understand the sources of atmospheric NOX and the processes that produce atmospheric nitrate. The stable isotope method is an effective analytical method for exploring the sources of NO3− in the atmosphere. This study discusses the range and causes of δ15N data from various sources of NOX emissions, provides the concepts of stable isotope techniques applied to NOX traceability, and introduces the use of Bayesian mixture models for the investigation of NOX sources. The combined application of δ15N and δ18O to determine the pathways of nitrate formation is summarized, and the contribution of Δ17O to the atmospheric nitrate formation pathway and the progress of combining Δ17O simulations to reveal the atmospheric oxidation characteristics of different regions are discussed, respectively. This paper highlights the application results and development trend of stable isotope techniques in nitrate traceability, discusses the advantages and disadvantages of stable isotope techniques in atmospheric NOX traceability, and looks forward to its future application in atmospheric nitrate pollution. The research results could provide data support for regional air pollution control measures.