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Plants
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Nutrient Management on Soil Microbiome Dynamics and Plant Health
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Nutrient Management on Soil Microbiome Dynamics and Plant Health

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant–Soil Interactions".

Deadline for manuscript submissions: 31 March 2026 | Viewed by 8501

Special Issue Editor

Dr. Chenliang Yu

E-Mail Website
Guest Editor
College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
Interests: phytohormones; soil microorganisms; plant nutrition; transcriptional regulation

Special Issue Information

Dear Colleagues,

Located at the intersection of agricultural science and ecology, nutrient management is emerging as a key strategy, gradually revealing its profound impact on the dynamics of soil microbial communities and plant health. Research in this field not only delves into how nutrients subtly regulate the diversity and activity of soil microbes but also elucidates how these microbial communities, in turn, affect plant growth, development, and resilience. From a scientific perspective, nutrient management directly influences microbial metabolic pathways and community structure by precisely regulating the supply of essential elements such as carbon, nitrogen, and phosphorus in the soil. This bottom-up control mechanism optimizes the efficiency of nutrient utilization by microbes and promotes the proliferation of beneficial microorganisms, thereby fostering a healthier and more stable soil ecosystem. In practical applications, effective nutrient management strategies have been widely adopted to enhance crop yield and quality. By applying organic fertilizers, biofertilizers, and precise chemical fertilizer formulations, farmers have successfully improved soil fertility, reduced the incidence of pests and diseases, and significantly boosted plants’ resistance to stresses such as drought and salinity.

Looking ahead, we can anticipate more refined management strategies to achieve sustainable optimization of soil ecosystems, providing robust technological support for the green transition and the sustainable development of global agriculture.

Dr. Chenliang Yu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • nutrient management
  • soil microbiome
  • microbial community dynamics
  • plant health
  • soil fertility
  • organic fertilizers
  • biofertilizers
  • chemical fertilizers
  • carbon, nitrogen, phosphorus cycling
  • plant–microbe interactions
  • soil health
  • abiotic stress resilience (salinity)

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Published Papers (6 papers)

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Research

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14 pages, 1118 KiB  
Article
Microbial-Mediated Soil Nutrient Enhancement in Moso Bamboo–Liquidambar formosana vs. Phoebe chekiangensis Mixed Plantings
by Anming Zhu, Lili Fan, Gang Lu, Liangjin Yao and Jianzhong Fan
Plants 2025, 14(12), 1868; https://doi.org/10.3390/plants14121868 - 18 Jun 2025
Viewed by 327
Abstract
This study investigated how Moso bamboo (Phyllostachys edulis)–broadleaf mixed forests influence soil properties and microbial communities to support ecological function and sustainable bamboo forest management. Three forest types were examined: pure Moso bamboo stands (MB) and mixed stands with Liquidambar formosana [...] Read more.
This study investigated how Moso bamboo (Phyllostachys edulis)–broadleaf mixed forests influence soil properties and microbial communities to support ecological function and sustainable bamboo forest management. Three forest types were examined: pure Moso bamboo stands (MB) and mixed stands with Liquidambar formosana (LB) or Phoebe chekiangensis (PB). Soil chemical properties, microbial diversity, and community composition were assessed using high-throughput sequencing, and functional taxa were correlated with soil nutrients. The results showed that mixed forests significantly influenced soil chemical properties. PB showed the lowest pH and highest total nitrogen (TN), while MB exhibited the highest soil organic matter (SOM) and total potassium (TK). LB maintained moderate TN, high SOM and TK, and stable pH, indicating a balanced nutrient profile. Although α-diversity did not differ significantly, β-diversity analysis revealed distinct microbial community structure (p < 0.01). LB was enriched with carbon-decomposing taxa (Terriglobales and Sphingomonas), PB with acid-tolerant, nitrogen-cycling groups (Candidatus Binatus), and MB with nitrogen-fixing taxa (Nitrobacteraceae and Bradyrhizobium). Co-occurrence network and functional pathway analyses indicated group-specific microbial associations and greater metabolic diversity in LB and PB. In conclusion, mixed Moso bamboo with broadleaf species significantly modified soil chemical properties and microbial community structure, with the Moso bamboo—L. formosana combination showing potential for improving soil nutrient status and microbial function. Full article
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
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18 pages, 3263 KiB  
Article
Integrated Microbiology and Metabolomics Analysis Reveal Responses of Soil Bacterial Communities and Metabolic Functions to N-Zn Co-Fertilization in the Rhizosphere of Tea Plants (Camellia sinensis L.)
by Min Lu, Yali Shi, Dandan Qi, Qiong Wang, Haowen Zhang, Ying Feng, Zhenli He, Chunwang Dong, Xiaoe Yang and Changbo Yuan
Plants 2025, 14(12), 1811; https://doi.org/10.3390/plants14121811 - 12 Jun 2025
Viewed by 640
Abstract
The co-fertilization of nitrogen (N) and zinc (Zn) offers significant advantages in improving the growth and development of tea plants (Camellia sinensis L). However, the corresponding responses of rhizosphere microecology remain unclear. In this study, a pot experiment was performed to investigate [...] Read more.
The co-fertilization of nitrogen (N) and zinc (Zn) offers significant advantages in improving the growth and development of tea plants (Camellia sinensis L). However, the corresponding responses of rhizosphere microecology remain unclear. In this study, a pot experiment was performed to investigate the effects of N-Zn co-fertilization on rhizosphere soil’s N availability, the rhizobacterial community and the metabolism of tea plants. N-Zn co-fertilization significantly increased the soil total of N, NH4+-N and NO3−-N contents. 16S rRNA sequencing found that N-Zn co-fertilization recruited rhizobacteria associated with N cycling and Zn activation, including Proteobacteria, Acidobacteriota and Gemmatimonadota, resulting in complex rhizobacterial networks. Metabolomics analysis indicated obvious interferences in the metabolisms of lipids, amino acids and cofactors and vitamins after fertilization. PLS-PM analysis suggested that fertilization had both direct and indirect influences on the rhizobacterial community and differential metabolites. RDA models identified pH (R2 = 0.734, p < 0.01; R2 = 0.808, p < 0.01) and total N (R2 = 0.633, p < 0.05; R2 = 0.608, p < 0.01) as dominant factors influencing both the rhizobacterial community and differential metabolites. Finally, network analysis found significant associations between rhizobacteria related to N cycling and Zn mobilization and metabolic processes involved in N metabolism and responses to Zn stress. These findings underscored that appropriate N-Zn co-fertilization is crucial for the rhizosphere soil’s N availability and the microenvironment of tea plants. Full article
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
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18 pages, 41343 KiB  
Article
Spatiotemporal Dynamics and Drivers of Vegetation Carbon Sinks in Zhejiang Province: A Case Study in Rapidly Urbanizing Subtropical Ecosystems
by Juntao Xu, Nguyễn Thị Hằng, Mengqi Ran and Junqia Kong
Plants 2025, 14(7), 1151; https://doi.org/10.3390/plants14071151 - 7 Apr 2025
Viewed by 592
Abstract
As a national ecological civilization pilot, Zhejiang’s growing vegetation carbon sink capacity is important for both regional ecological security and China’s carbon neutrality goals, but current studies lack a comprehensive assessment of multi-factor interactions. This study employed an improved Carnegie–Ames–Stanford Approach (CASA) and [...] Read more.
As a national ecological civilization pilot, Zhejiang’s growing vegetation carbon sink capacity is important for both regional ecological security and China’s carbon neutrality goals, but current studies lack a comprehensive assessment of multi-factor interactions. This study employed an improved Carnegie–Ames–Stanford Approach (CASA) and soil respiration empirical equation to estimate Net Ecosystem Productivity (NEP) in Zhejiang Province, and trend analysis, partial correlation analysis, and the GeoDetector model based on optimal parameters (OPGD) were utilized to investigate the spatiotemporal variations and driving factors of vegetation NEP. The results showed that the multi-year average NEP and carbon sink capacity in Zhejiang Province were 387.67 g C m−2 a−1 and 38.84 Tg C a−1, exhibiting an increasing trend at an average rate of 2.15 g C m−2 a−1 and 0.23 Tg C a−1, respectively. Spatially, NEP was higher in the western and southern mountainous regions and lower in the eastern coastal and northern plains. NEP in Zhejiang Province was driven by both natural and anthropogenic factors, with NDVI (q = 0.502) and elevation (q = 0.373) being the primary natural drivers, and nighttime light intensity (q = 0.327) and impervious surface dynamics (q = 0.295) being the main anthropogenic drivers. Moreover, the interactions among these factors all exhibited synergistic enhancement effects. Overall, Zhejiang Province functioned predominantly as a carbon sink, with its sequestration capacity gradually strengthening over time. The combined effects of natural and anthropogenic factors drove the spatiotemporal heterogeneity of vegetation NEP. These findings highlight the importance of coordinated ecosystem management strategies that consider both natural and anthropogenic-induced impacts to enhance the achievement of regional carbon sink goals. Full article
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
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16 pages, 4758 KiB  
Article
Soil Microbial and Metabolomic Shifts Induced by Phosphate-Solubilizing Bacterial Inoculation in Torreya grandis Seedlings
by Yi Li, Yuanyuan Guan, Zhengchu Jiang, Qiandan Xie, Qi Wang, Chenliang Yu and Weiwu Yu
Plants 2024, 13(22), 3209; https://doi.org/10.3390/plants13223209 - 15 Nov 2024
Cited by 1 | Viewed by 1132
Abstract
Phosphorus is crucial for plant growth and development, but excess fertilizer not absorbed by plants often binds with metal ions like iron and manganese, forming insoluble compounds that contribute to soil environmental pollution. This study investigates the impact of Burkholderia sp., a phosphate-solubilizing [...] Read more.
Phosphorus is crucial for plant growth and development, but excess fertilizer not absorbed by plants often binds with metal ions like iron and manganese, forming insoluble compounds that contribute to soil environmental pollution. This study investigates the impact of Burkholderia sp., a phosphate-solubilizing bacterium utilized as a biofertilizer, on the fertility of T. grandis soil, alongside the associated shifts in soil metabolites and their relationship with microbial communities after inoculation. The soil microbial community structures and metabolite profiles were analyzed via amplicon sequencing and high-resolution untargeted metabolomics. The inoculation of phosphate-solubilizing bacteria led to a significant (p < 0.05) enhancement in total phosphorus, potassium, and nitrogen concentrations in the soil, with a marked increase in available phosphorus in bulk soil (p < 0.05). Moreover, the microbial community structure exhibited significant shifts, particularly in the abundance of bacterial phyla such as Acidobacteria, Chloroflexi, Proteobacteria, and the fungal phylum Ascomycota. Metabolomic analysis revealed distinct metabolites, including fatty acids, hormones, amino acids, and drug-related compounds. Key microbial taxa such as Chloroflexi, Proteobacteria, Acidobacteria, Verrucomicrobia, Mucoromycota, and Ascomycota indirectly contributed to soil phosphorus metabolism by influencing these differential metabolites. In conclusion, the application of phosphate-solubilizing bacteria offers an innovative approach to improving soil quality in T. grandis, promoting phosphorus utilization efficiency, and enhancing soil ecosystem health by optimizing microbial communities and metabolite compositions. Full article
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
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20 pages, 8830 KiB  
Article
Enhanced Antifungal Efficacy of Validamycin A Co-Administered with Bacillus velezensis TCS001 against Camellia anthracnose
by Zhilei Chen, Hao Cao, Jing Jin, Zhong Li, Shouke Zhang and Jie Chen
Plants 2024, 13(19), 2743; https://doi.org/10.3390/plants13192743 - 30 Sep 2024
Cited by 1 | Viewed by 1288
Abstract
Anthracnose, a fungal disease harming fruit trees and crops, poses a threat to agriculture. Traditional chemical pesticides face issues like environmental pollution and resistance. A strategy combining low-toxicity chemicals with biopesticides is proposed to enhance disease control while reducing chemical use. Our study [...] Read more.
Anthracnose, a fungal disease harming fruit trees and crops, poses a threat to agriculture. Traditional chemical pesticides face issues like environmental pollution and resistance. A strategy combining low-toxicity chemicals with biopesticides is proposed to enhance disease control while reducing chemical use. Our study found that mixing validamycin A (VMA) and Bacillus velezensis TCS001 effectively controlled anthracnose in Camellia oleifera. The combination increased antifungal efficacy by 65.62% over VMA alone and 18.83% over TCS001 alone. It caused pathogen deformities and loss of pathogenicity. Transcriptomic analysis revealed that the mix affected the pathogen’s metabolism and redox processes, particularly impacting cellular membrane functions and inducing apoptosis via glycolysis/gluconeogenesis. In vivo tests showed the treatment activated C. oleifera’s disease resistance, with a 161.72% increase in polyphenol oxidase concentration in treated plants. This research offers insights into VMA and TCS001’s mechanisms against anthracnose, supporting sustainable forestry and national edible oil security. Full article
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
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Review

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14 pages, 1186 KiB  
Review
The Role of Phosphate-Solubilizing Microbial Interactions in Phosphorus Activation and Utilization in Plant–Soil Systems: A Review
by Ying Zhu, Yijing Xing, Yue Li, Jingyi Jia, Yeqing Ying and Wenhui Shi
Plants 2024, 13(19), 2686; https://doi.org/10.3390/plants13192686 - 25 Sep 2024
Cited by 8 | Viewed by 3735
Abstract
To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant–soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. [...] Read more.
To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant–soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency. Full article
(This article belongs to the Special Issue Nutrient Management on Soil Microbiome Dynamics and Plant Health)
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