The effects of nitrogen fertilizer addition on soil microbial community characteristics and ecosystem multifunctionality

The gap

Evidence profile

Sourced from the future work and future-work section and abstract of the source papers, classified as general, drawn from work published between 2025 and 2026, spanning 7 journals. Those papers have been cited 48 times in total.

Supporting evidence — 8 representative gaps

• Microbial biostimulants for plant stress tolerance and climate-resilient agriculture from mechanisms to recent advances and future perspectives (2026) · Discover Sustainability · doi

  This review highlights the considerable potential of MBs, particularly PGPR and AMF, to enhance nutrient acquisition, plant growth, stress tolerance, and crop productivity through diverse physiological, biochemical, and molecular mechanisms. By improving resource-use efficiency and reducing dependence on synthetic fertilizers and pesticides, MBs represent a promising component of sustainable, climate-resilient, and regenera- tive agricultural systems. However, their widespread adoption will depend on improving their consistency, reliability, and performance under diverse field conditions. To maximize this potential, future research should focus on elucidating the molecu- lar mechanisms underlying plant–microbe interactions through integrated multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics. A better understanding of plant genotype × microbial strain × environment interactions Mazhar et al. Discover Sustainability (2026) 7:1473 Page 17 of 26 will facilitate the identification of robust microbial candidates with consistent perfor- mance across diverse agroecosystems. In parallel, greater emphasis should be placed on developing standardized and stable formulations, optimizing application strategies, and validating their efficacy through long-term, multi-location field trials to improve prod- uct reliability, cost-effectiveness, and commercial scalability. Beyond technological advances, future efforts should also address the broader envi- ronmental and socioeconomic implications of MB adoption. Integrating MBs into climate-smart and regenerative agricultural systems has the potential to improve soil health, restore soil biological functions, enhance resource-use efficiency, reduce green- house gas emissions associated with synthetic fertilizer use, strengthen food security, and support sustainable agricultural intensification. However, successful implementa- tion will depend on supportive regulatory frameworks, effective technology transfer, increased farmer awareness and adoption, and clear demonstration of the economic benefits of MBs under diverse agricultural conditions. Achieving these goals will require close collaboration among researchers, industry, policymakers, extension services, and farmers to accelerate the development, validation, and widespread adoption of reliable microbial biostimulant technologies.

  generalfuture workevidence 5/5
  Keywords: diverse agricultural adoption potential plant microbial enhance mechanisms improving resource efficiency synthetic sustainable climate systems
• Root exudates in controlled environment agriculture: composition, function, and future directions (2025) · Frontiers in Plant Science · cited 31× · doi

  Deniz Camli-Saunders and Camilo Villouta* Controlled Environment Agriculture Lab, Department of Plant Sciences and Entomology, University of Rhode Island, Kingston, RI, United States Two decades of research has revealed an intricate network of root exudates in plants, which they use to interact with and mediate their surrounding environment, the rhizosphere. Prior research has been conducted mainly on model plants such as Arabidopsis or staple monoculture crops like maize, soybean, and rice, revealing crucial roles in plant growth, microbiota interaction, nutrient acquisition, and bioremediation. However, similar research has only begun to be conducted in Controlled Environment Agriculture (CEA) systems, leaving a considerable knowledge gap in the mechanisms, impacts, and uses of exudates in CEA. Exhaustive literature searches revealed less than two dozen articles with direct implications in CEA vegetable crop exudates. This review synthesizes the existing literature to examine the composition, functions, and influences of vegetable root exudates within CEA systems. The first section explores key compounds —including amino and organic acids, and sugars— interactions. The second along with mechanistic processes, and microbial section compares root exudates in soil-based versus hydroponic CEA systems based upon differences in substrate, (a)biotic stressors, microorganisms, and nutrient availability. By contrasting existing literature on both CEA soil-based and hydroponic systems, the section examines likely differences in exudate composition, mechanisms, and functions. The final section presents case studies from both hydroponic and soil based systems, highlighting how root exudates contribute to environmental stress mitigation, allelopathy, disease response, bio/phytoremediation, and pest control. It reveals major avenues for the use of exudates in CEA systems worldwide. Lastly, we ponder the future avenues of exploration for CEA root exudates, proposing the creation of a database for usage in smaller or organic farms and in urban agriculture settings. In conjunction, we emphasize the need for further investigation into the potential of exogenous applications of exudate-like compounds to positively impact yield, disease resistance, soil restoration, and land reclamation, especially in the context of climate change. KEYWORDS root exudates, rhizosphere interactions, allelopathy, microbiota interactions, hydroponics, controlled environment agriculture (CEA), soil-based agriculture

  generalfuture workevidence 5/5
  Keywords: exudates root systems agriculture soil based environment controlled literature interactions hydroponic plant revealed plants rhizosphere
• Physiological Mechanisms of Plant Growth-Promoting Rhizobacteria in Enhancing Abiotic Stress Tolerance of Vegetable Crops: A Review (2026) · Plants · cited 9× · doi

  Plant growth-promoting rhizobacteria (PGPR) regulate the physiological metabolic network of host plants under abiotic stress through multi-dimensional mechanisms [112]. The core of PGPR is to construct a mutually beneficial “plant–microorganism” functional consortium. On the one hand, PGPR directly strengthen the ability of plants to absorb water and mineral nutrients by secreting metabolites such as organic acids and siderophores and regulating root architecture, thereby alleviating osmotic imbalance and nutrient deficiency caused by stress [113]. On the other hand, PGPR, as key biological “elicitor”, can systemati- cally activate the endogenous defense system of plants, including increasing the activities of antioxidant enzymes such as superoxide dismutase (SOD) and peroxidase (POD), to remove excessive reactive oxygen species (ROS), reduce membrane lipid peroxidation damage, and induce the accumulation of osmotic regulators such as proline to maintain cell homeostasis [114]. More importantly, PGPR can reshape the rhizosphere microenviron- ment, and its metabolites can be used as signal molecules or nutrient substrates to attract and enrich other beneficial microorganisms, thus forming a more resistant rhizosphere microbial community [115]. https://doi.org/10.3390/plants15050686 Plants 2026, 15, 686 12 of 18 Although the great potential of PGPR has been verified in many crops, there are still significant gaps in its research and application in vegetable crops. At present, the efficient PGPR resources isolated and identified from the rhizosphere of vegetable crops are still relatively limited, mainly concentrated in several common genera such as Pseudomonas, Bacillus, and Enterobacter, and there is a unique core microbiome that has not been fully ex- cavated. In recent years, technologies such as high-throughput sequencing and culturomics have overcome the restrictions of traditional isolation and culture techniques, revealing that under drought, high-salt, and other stresses, the rhizosphere metabolic spectrum of vegetable crops undergoes specific changes and drives the directional enrichment of stress-tolerant functional microorganisms [116]. Therefore, the directional screening of PGPR from adversity has become an effective strategy for obtaining highly active strains. However, the exploration of microbial resources in extreme environments still faces the challenges of difficult sample acquisition and low culturability of strains; therefore, the development new in situ culture and fidelity identification techniques is urgent. At present, the biggest obstacle to the application of PGPR from laboratory to field is effect instability. The field growth-promoting and stress-resistant effects of strains with excellent performance under controllable conditions are often greatly reduced due to weak colonization ability, soil indigenous microbial competition, and fluctuations in environmental factors. In theory, the compound microbial agent can

  generalfuture workevidence 5/5
  Keywords: pgpr plants stress rhizosphere microbial crops still vegetable strains plant growth promoting metabolic core beneficial
• Harnessing the Rhizosphere Microbiome for Selenium Biofortification in Plants: Mechanisms, Applications and Future Perspectives (2025) · Microorganisms · cited 8× · doi

  Ruixin Fu 1, Mengyuan Zhu 1, Yanrong Zhang 1, Junmin Li 1 and Haichao Feng 2,* 1 School of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China; [email protected] (R.F.) 2 College of Agriculture, Henan University, Kaifeng 475004, China * Correspondence: [email protected] Abstract: The rhizosphere microbiome plays a critical role in promoting crop health and productivity. Selenium (Se), a beneficial trace element for plants, not only enhances resis- tance to both abiotic and biotic stresses but also modulates soil microbial communities. Se biofortification of crops grown in seleniferous soils using selenobacteria represents an eco-friendly and sustainable biotechnological approach. Crops primarily absorb selenium from the soil in its oxidized forms, selenate and selenite, and subsequently convert it into organic Se compounds. However, the role of Se-oxidizing bacteria in soil Se transformation, bioavailability, and plant uptake remains poorly understood. In this review, systematic collection and analysis of research on selenobacteria, including both Se-oxidizing and Se-reducing bacteria, are therefore essential to elucidate their functions in enhancing crop growth and health. These insights can (i) deepen our mechanistic understanding of mi- crobially mediated Se cycling and stress resilience and (ii) offer a novel framework for nanomicrobiome engineering aimed at promoting sustainable food production. Keywords: rhizosphere microorganisms; selenium biofortification; Se-oxidizing bacteria; colonization; crop health Academic Editor: Mohamed Hijri Received: 24 April 2025 Revised: 22 May 2025 Accepted: 26 May 2025 Published: 28 May 2025 Citation: Fu, R.; Zhu, M.; Zhang, Y.; Li, J.; Feng, H. Harnessing the

  generalfuture workevidence 5/5
  Keywords: crop health selenium soil oxidizing bacteria zhang feng food shangqiu university china rhizosphere role promoting
• Rhizosphere–Canopy Communication in Horticultural Crops: Root Gating, Systemic Signaling, and Links to Yield and Quality (2026) · Horticulturae · doi

  Rhizosphere effects reach horticultural canopies through distinct routes. Microbial nutrient mobilization and symbiosis alter the resources entering host transport systems; root perception and metabolic conversion generate hormonal or immune relays; and ionic, hydraulic, or electrical responses can propagate rapid changes in state. CEP–CEPR–CEPD, ABCG14-dependent cytokinin transport, and CLE25–BAM–ABA provide defined host transport architectures, whereas the root FMO1–UGT76B1–NHP circuit directly connects fungal inputs with shoot immunity and growth. These examples should not be read as a single pathway universally activated by beneficial microbes. The root-gating framework contributes a testable distinction between exposure in the rhizosphere and the resources or signals that leave the root. Selective entry, surface perception, and metabolic transformation can produce different outputs from the same input. In leaves, these outputs couple transcription and metabolism to carbon assimilation, water relations, and defense. Their horticultural consequences depend on source–sink allocation and on metabolism within the harvested organ. Field studies support effects on fruit carotenoids, soluble solids, and processing composition, but also include unchanged yield and treatment- or season-dependent quality responses. A microbial effect on one of these traits cannot establish simultaneous improvement of all of them. Three priorities connect these mechanisms to horticultural application. First, distin- guish direct microbial-molecule transport from host-mediated relays using source-resolved tracing and functional intervention. Second, link root and leaf measurements to fruit-local metabolism, marketable yield, composition, and, where relevant, storage or ornamental https://doi.org/10.3390/horticulturae12101211 Horticulturae 2026, 12, 1211 16 of 22 endpoints. Third, validate the response across cultivars, rootstocks, management regimes, and seasons, while measuring carbon-allocation and exudation feedbacks. Claim-specific evidence grades make clear which links are established and which remain hypotheses. This approach supports microbial selection for defined production goals rather than assuming a universal growth-and-quality benefit. Author Contributions: M.J., H.L., G.N., L.G., Y.Y., J.X., L.L. and B.H. contributed to the study conception and design. Material preparation, data collection, and analysis were performed by M.J. The first draft of the manuscript was written by M.J. All authors have read and agreed to the published version of the manuscript. Funding: This work was supported by HAAFS Agriculture Science and Technology Innovation Project (2026KJCXZX-CGS-7), the earmarked fund for CARS (CARS-28-27) and the Domestic Further Study and Training Program for Young Scientific and Technological Talents of the Hebei Academy of Agriculture and Forestry Sciences. Data Availability Statement: No new data were created or analyzed in this study. Data sharing is not applicable to this article. Acknowledgments: OpenAI Codex (https://help.openai.com/en/collections/14937394-codex (ac- cessed on 22 September 2026)) was used to assist with the visual design and rendering of the graphical abstract. The authors have reviewed and edited the output and take full responsibility for the content of this publication. Conflicts of Interest: The authors declare no conflicts of interest.

  generalfuture workevidence 5/5
  Keywords: root microbial transport horticultural host metabolism authors rhizosphere effects resources perception metabolic relays responses dependent
• Alfalfa-mediated phytoremediation and soil restoration for sustainable cereal and fruit crop production: a review of roles, detoxification mechanisms, nitrogen enhancement, and agroecological integration (2026) · Frontiers in Sustainable Food Systems · doi

  This review demonstrates that physiological detoxification mechanisms, rhizosphere microbiome management, and agro- nomic intercropping provide a comprehensive pathway for sustain- able cereal and fruit crop production. Below-ground interactions show that alfalfa roots alter rhizosphere chemistry by releasing specialized exudates, chelating toxic ions, and recruiting plant growth-promoting microbes (PGPM) and AMF. These biological networks mitigate environmental stressors by upregulating anti- oxidant enzyme activities (e.g., superoxide dismutase and catalase) and accumulating protective osmolytes like soluble sugars and pro- teins. Alfalfa transcends its traditional identity as the “Queen of Forages” to serve as a multifunctional biological soil engineer, inte- grating agronomic productivity with ecological restoration through biological nitrogen fixation, soil restructuring, carbon sequestra- tion, and enhanced water retention. By acting as a break crop and functional insectary, it disrupts pest and disease cycles while fos- tering resilient, resource-efficient cropping systems capable of withstanding drought, heat, and salinity. In cereal systems, alfalfa rotations enhance nitrogen-use effi- ciency, reduce fertilizer requirements, and improve subsequent yields, with land equivalent ratios exceeding 1.0 in intercropping. In fruit orchards, alfalfa contributes to tree nitrogen requirements, improves soil moisture retention, and generates early economic returns through forage production. Long-term alfalfa introduction improves soil struc- tural stability through stable micro- and macro-aggregate formation, enhancing water retention and nutrient cycling in semi-arid and degraded landscapes. Alfalfa demonstrates phytoremediation potential for heavy metals, petroleum hydrocarbons, and pesticide residues via phyto- extraction, phytostabilization, and rhizodegradation, supported by coordinated molecular responses involving CYP450s, GSTs, and metal transporters. Integration with PGPR, AMF, and biochar amplifies these pathways, particularly in cereal rotations. However, critical evidence gaps remain: direct links between contaminant removal and subsequent crop yield, quality, and safety are often inferred rather than demonstrated, especially in fruit systems where field validation in mature orchards and vineyards is scarce. Contaminated biomass requires rigorous safety screening, as atten- uation does not guarantee feed or food safety. Trade-offs include potential resource competition, soil acidification, and altered nitro- gen-cycling communities that may increase N₂O emissions, neces- sitating context-specific management. Future priorities should focus on: (1) developing specialized alfalfa cultivars for enhanced hyperaccumulation, phytostabiliza- tion, and nitrogen-fixation under abiotic stress; (2) exploiting CRISPR/Cas9 to edit genes controlling root architecture, exudate profiles, and stress tolerance; (3) scaling multi-species PGPM and AMF consortia with organic amendments to reduce fertilizer requirements while enhancing ecological stability; (4) long-term field trials in Mediterranean and Loess Plateau environments inte- grating contaminant mass balance with crop performance and food safety; (5) nano-enabled strategies and multi-omics-driven geno- type selection for site-specific remediation; and (6) climate-adap- tive management balancing water conservation with productivity. Incentivizing adoption through ecological restoration programs requires targeted financial mechanisms (subsidies, reduced-interest loans, yield-adjustment compensation), technical capacity-building, risk-management tools, and secure land-tenure rights. Bridging eco- nomic viability with ecological stewardship will mitigate climate change, curb fertilizer runoff, and secure global food production. Realizing alfalfa’s full potential demands a shift from short-term observations to long-term, multi-site field trials evaluating contami- nant mass balances, microbial persistence, biomass safety, and crop productivity, ensuring alfalfa-based systems contribute to climate- resilient, resource-efficient, and safe agricultural production globally.

  generalfuture workevidence 5/5
  Keywords: alfalfa crop soil safety management production ecological nitrogen systems term cereal fruit biological productivity water
• Boron and Selenium Combine to Alleviate Cadmium Stress and Improve Quality and Yield of Cherry Tomatoes (2026) · Journal of Plant Growth Regulation · doi

  Mechanistic elucidation via transcriptomic/ proteomic analyses to identify key regulated genes (e.g., HMA, Nramp) and pathways; Field validation trials to assess the stability, optimal dosage, and economic feasibility across diverse agroecosystems; Investigation of long-term effects on soil health and elemental residues to ensure sustainability

  generalfuture-work sectionevidence 5/5
  Keywords: mechanistic elucidation via transcriptomic proteomic analyses identify key
• Drought–salinity interaction suppresses seed germination and seedling growth in alfalfa by altering water status, membrane stability, and antioxidant responses (2026) · Frontiers in Plant Science · doi

  However, the integrated responses of alfalfa during early establishment to combined drought and salinity stress, particularly the physiological links among water status, membrane stability, antioxidant defense, seed germination, and seedling growth, remain insufficiently understood.

  generalabstractevidence 4/5
  Keywords: integrated responses alfalfa early establishment combined drought salinity stress particularly physiological links among water status

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