Ammonium Biology: From Molecular Response to Fertilization

Abstract submission deadline

31 October 2026

Manuscript submission deadline

31 December 2026

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Topic Information

Dear Colleagues,

We would like to invite you to contribute to the Topic "Ammonium Biology: From Molecular Response to Fertilization". Ammonium (NH4+) is a key nitrogen source in soils, yet it can be toxic at moderate concentrations, particularly when used as the primary nitrogen source. To address this challenge, our topic aims to explore how plants respond to ammonium and how genetic breeding or agronomic improvements can enhance crop tolerance to NH4+ fertilizers, thereby improving application efficiency. This topic will cover: (i) Plant Tolerance to Ammonium: Investigating recent advances in enhancing plant tolerance to NH4+ nutrients to improve nitrogen availability and plant health. (ii) Environmental Interactions: Examining the interactions between NH4+ nutrition and environmental factors, such as CO₂ and O₃ levels, droughts, high-temepratures, light, and heavy metal toxicity. (iii) Fertilizer Application and Agronomy: Analyzing the impact of different NH4+-N fertilizer forms and agronomic practices on utilization efficiency and plant tolerance. We seek comprehensive studies, reviews, brief reports, and communications that present the latest findings in plant responses to NH4+, from molecular mechanisms to practical fertilizer applications.. We look forward to your valuable contributions to this exciting and impactful field.

Dr. Dong-Wei Di
Dr. Soichi Kojima
Prof. Dr. Byoung Ryong Jeong
Prof. Dr. Monika Skowrońska
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	4.5	7.8	2011	17.4 Days	CHF 2600	Submit
Agronomy agronomy	4.1	7.6	2011	17.7 Days	CHF 2600	Submit
Environments environments	4.3	5.7	2014	18.6 Days	CHF 1800	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.5 Days	CHF 2900	Submit
Nitrogen nitrogen	2.8	3.4	2020	18.1 Days	CHF 1200	Submit
Plants plants	4.7	8.5	2012	14.8 Days	CHF 2700	Submit

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Published Papers (5 papers)

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All Agriculture Agronomy Environments IJMS Nitrogen Plants

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16 pages, 5953 KB  

Open AccessArticle

Shifts in Abiotic and Biotic Factors Correlate with Changes in Bacterial and Fungal Network Assembly Under Straw Incorporation Across Three Soil Depths

by Wei Chen, Mengyuan Wen, Meiyu Chu, Yongfei Wei, Siyao Huang, Chunjuan Wang and Jinlong Wang

Agriculture 2026, 16(12), 1253; https://doi.org/10.3390/agriculture16121253 - 6 Jun 2026

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Abstract

Crop residue management strongly influences soil microbial communities, yet the mechanisms by which it regulates microbial co-occurrence network assembly across soil profiles remain poorly understood. Here, we investigated the effects of three straw management practices—no straw return (CK), straw burning (BS), and deep [...] Read more.

Crop residue management strongly influences soil microbial communities, yet the mechanisms by which it regulates microbial co-occurrence network assembly across soil profiles remain poorly understood. Here, we investigated the effects of three straw management practices—no straw return (CK), straw burning (BS), and deep plowing with straw incorporation (DPS)—on soil physicochemical properties, microbial diversity, and co-occurrence network structure across multiple soil depths in a Mollisol of Northeast China. By integrating high-throughput sequencing, network analysis, and structural equation modeling (SEM), we explored the correlative relationships associated with microbial network assembly. DPS significantly correlates with higher soil organic carbon content, nutrient availability, and moisture content, particularly in subsoil layers. Under DPS, we obtained more complex and robust microbial networks characterized by higher connectivity and clustering. In contrast, under BS, we found reduced network complexity and stability. SEM may suggest the presence of distinct assembly mechanisms between microbial groups: bacterial network structure models responded to soil physicochemical properties, suggesting strong environmental filtering, whereas shifts in fungal network structures correlate with alpha diversity, highlighting the importance of biotic regulation. Notably, under the evaluated conditions, beta diversity was positively associated with network structural attributes across both groups, indicating potential links between community compositional variation and microbial co-occurrence patterns. These findings suggest that straw incorporation may be associated with shifts in microbial co-occurrence network attributes under the evaluated field conditions. However, the observed relationships are primarily correlative and based on statistical modeling approaches. The underlying ecological mechanisms linking soil properties, microbial diversity, and network structure require further validation through controlled biochemical, physiological, and experimental studies. This study provides additional ecological insights into soil microbial responses to residue management and highlights the potential role of residue management in shaping microbial network stability under the evaluated field conditions. Full article

(This article belongs to the Topic Ammonium Biology: From Molecular Response to Fertilization)

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17 pages, 3275 KB  

Open AccessArticle

Deconfounding Phenology in SPAD-Based Rice Nitrogen Diagnosis Using Physiological Time and Canopy-Stratified Measurements

by Chengyingying Qin, Haitao Xiang, Qiaoyi Huang and Yuan Wang

Plants 2026, 15(4), 591; https://doi.org/10.3390/plants15040591 - 13 Feb 2026

Cited by 2 | Viewed by 535

Abstract

Phenology can confound rice nitrogen diagnosis based on SPAD readings because leaf greenness and nitrogen concentration change nonlinearly with development. We tested whether physiological time, expressed as growing degree days (GDD), can reduce this developmental bias and improve the portability of SPAD-based diagnosis. [...] Read more.

Phenology can confound rice nitrogen diagnosis based on SPAD readings because leaf greenness and nitrogen concentration change nonlinearly with development. We tested whether physiological time, expressed as growing degree days (GDD), can reduce this developmental bias and improve the portability of SPAD-based diagnosis. We analyzed 1141 observations from 20 independent field experiments across five sites, spanning japonica, indica, and hybrid cultivars and nitrogen fertilizer treatments (0–300 kg N ha⁻¹). SPAD was measured on up to five leaf-from-top positions (LFT1–LFT5) and used to predict leaf nitrogen concentration (LNC), plant nitrogen concentration (PNC), and nitrogen nutrition index (NNI). Across group-wise cross-validation by experiment, adding GDD to SPAD consistently improved cross-environment accuracy (mean R² up to 0.75 for LNC and 0.79 for PNC) and markedly weakened residual trends along GDD. Multiplicative SPAD×GDD degraded performance, while explicit interaction terms provided little gain over a simple additive SPAD + GDD form. Interpretable analyses further showed that diagnostic information is concentrated in mid-canopy leaves and shifts with physiological time. Combining GDD with a two-leaf SPAD protocol retained most accuracy for concentration targets, supporting a time-aligned and field-practical approach for robust nitrogen diagnosis. Full article

(This article belongs to the Topic Ammonium Biology: From Molecular Response to Fertilization)

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22 pages, 5949 KB  

Open AccessArticle

Genome-Wide Analysis of Ammonium Transporter Genes in Flowering Chinese Cabbage and Functional Insights into BcAMT1.1 Under Low-Nitrogen Conditions

by Yunna Zhu, Lihua Zhong, Qiuxiang Zhong, Xinmin Huang, Ali Anwar, Wei Su, Riyuan Chen and Shiwei Song

Plants 2025, 14(24), 3812; https://doi.org/10.3390/plants14243812 - 14 Dec 2025

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Abstract

As a primary macronutrient, nitrogen is integral to plant growth and regulates their development; ammonium transporters (AMTs) mediate nitrogen absorption and its involvement in metabolism. In this study, nine BcAMT genes were identified in flowering Chinese cabbage (Brassica campestris) and were [...] Read more.

As a primary macronutrient, nitrogen is integral to plant growth and regulates their development; ammonium transporters (AMTs) mediate nitrogen absorption and its involvement in metabolism. In this study, nine BcAMT genes were identified in flowering Chinese cabbage (Brassica campestris) and were systematically categorized into two subfamilies. Their evolutionary relationships, conserved motifs, chromosomal distribution, cis-regulatory elements, and expression profiling were systematically characterized. RNA sequencing and quantitative real-time PCR (qRT-PCR) analyses demonstrated that BcAMT1.1 was abundantly expressed in roots, leaves, and stems of flowering Chinese cabbage and was markedly upregulated under nitrogen deficiency. Assessing subcellular location using GFP fusion demonstrated that BcAMT1.1 localized to the plasma membrane. Functional assays identified heterologous expression in the yeast mutant strain 31019b, and transgenic Arabidopsis validated that BcAMT1.1 acted as a functional ammonium transporter. Compared with the wildtype, overexpressing BcAMT1.1 promoted seedling growth, enhanced NH₄⁺ influxes and NO₃⁻ effluxes under low-nitrogen conditions, and significantly increased the transcription levels of key nitrogen assimilation genes (i.e., AtGLN1.1, AtGLN2, AtGDH2). Collectively, our findings enhance the fundamental understanding of BcAMT gene functions and highlight BcAMT1.1 as a crucial component in nitrogen uptake and assimilation under low-nitrogen conditions, providing valuable genetic resources for improving nitrogen efficiency in vegetable crops. Full article

(This article belongs to the Topic Ammonium Biology: From Molecular Response to Fertilization)

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21 pages, 2438 KB  

Open AccessArticle

Organic Fertilization Enhances Microbial-Mediated Dissolved Organic Matter Composition and Transformation in Paddy Soil

by Long Chen, Huajun Fang, Shulan Cheng, Hui Wang, Yifan Guo, Fangying Shi, Bingqian Liu and Haiguang Pu

Agriculture 2025, 15(23), 2412; https://doi.org/10.3390/agriculture15232412 - 22 Nov 2025

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Abstract

Dissolved organic matter (DOM) is a crucial carbon source for soil microorganisms and plays a vital role in nutrient cycling and carbon (C) sequestration in soils. However, the extent to which soil microbes mediate DOM transformation at the molecular level, and whether this [...] Read more.

Dissolved organic matter (DOM) is a crucial carbon source for soil microorganisms and plays a vital role in nutrient cycling and carbon (C) sequestration in soils. However, the extent to which soil microbes mediate DOM transformation at the molecular level, and whether this is regulated by different organic fertilization, remains unclear. Here, we designed a field experiment to investigate the transformations of DOM under three types of organic fertilization (straw, biochar, and manure) using Fourier transform ion cyclotron resonance mass spectrometry and metagenomic analysis. Compared to the control, manure fertilization increased the molecular chemodiversity of DOM by 33.2%, with recalcitrant compounds (e.g., highly unsaturated phenolic compounds and lignins) increasing by 47.2%. In contrast, labile compounds (e.g., aliphatics) decreased by 73.5%. Compared to straw treatment, manure application significantly increased the average conversion rate of dissolved organic matter (DOM). This process was accompanied by a significant increase in the Shannon index of the soil microbial community (p < 0.05) and upregulation of ABC transporter-encoding genes (e.g., livK, livM). DOM composition directly governed transformation potential (p < 0.01), whereas functional genes enhanced transformation indirectly by modulating DOM composition. This study elucidates microbial-mediated DOM transformation mechanisms under varying organic fertilization practices, providing a scientific basis for optimizing soil organic matter management in paddy ecosystems. Full article

(This article belongs to the Topic Ammonium Biology: From Molecular Response to Fertilization)

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24 pages, 4111 KB  

Open AccessArticle

Evaluation of the Performance of a Nitrogen Treatment Plant in a Continental Mediterranean Climate: A Spanish Pig Farm Case Study

by Laura Escudero-Campos, Francisco J. San José, María del Pino Pérez Álvarez-Castellanos, Adrián Jiménez-Sánchez, Berta Riaño, Raúl Muñoz and Diego Prieto-Herráez

Nitrogen 2025, 6(3), 68; https://doi.org/10.3390/nitrogen6030068 - 14 Aug 2025

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Abstract

This study presents a four-year evaluation (2020–2024) of an integrated climate mitigation project on a pig farm in Ávila, Spain, at an elevation of over 1100 m above sea level with continental climate conditions. The project aimed to reduce greenhouse gas emissions (GHG) [...] Read more.

This study presents a four-year evaluation (2020–2024) of an integrated climate mitigation project on a pig farm in Ávila, Spain, at an elevation of over 1100 m above sea level with continental climate conditions. The project aimed to reduce greenhouse gas emissions (GHG) and nitrogen pollution by implementing solid–liquid filtration followed by biological treatment in a 625 m³ Sequencing Batch Reactor (SBR) operating under a nitrification–denitrification (N-DN) regime. The SBR carried out four daily cycles, alternating aerobic and anoxic phases, with 5 and 8 m³ inlets. Aeration intensity and redox potential were continuously monitored to optimize bacterial activity. Analytical parameters (pH, electrical conductivity, solids content, nitrogen, phosphorus, and potassium) were measured using ISO methods and tracked frequently. Annual emission reductions were 75% for N₂O, up to 97% for NH₃, and 80% for N₂. In the summer months, we observed higher efficiency reduction for N₂, NH₃, and NO₂. Additionally, there was a 75% average reduction for COD and up to 92% for total GHG emissions. This real-world case study highlights the effectiveness of SBR-based N-DN systems for nutrient removal and emission reduction in high-altitude, climate-sensitive regions, contributing to EU nitrate directive compliance and circular economy practices. Full article

(This article belongs to the Topic Ammonium Biology: From Molecular Response to Fertilization)

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