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Microorganisms
Special Issues
Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition
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Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 3423

Special Issue Editors

Dr. Dan Xiao

E-Mail Website
Guest Editor
Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
Interests: nutrient cycling; vegetation recovery; microbial biodiversity; soil carbon; soil nitrogen
Special Issues, Collections and Topics in MDPI journals
Dr. Yinhang Xia

E-Mail Website
Guest Editor
College of Resources, Hunan Agricultural University, Changsha 410128, China
Interests: soil organic carbon; soil organic nitrogen cycling; microbial metabolic processes; agricultural ecosystems

Special Issue Information

Dear Colleagues,

Soil nutrient cycles involving microorganisms play a crucial role in enhancing soil fertility, promoting plant growth, controlling pathogens and pests, improving soil structure, and maintaining ecosystem functions. These processes are affected by environmental changes, such as global climate warming, nitrogen deposition, heavy metal pollution, waste disposal, and agricultural management practices. Understanding the role of soil microorganisms in organic matter turnover, nitrogen cycling, phosphorus transformations, and metal sequestration in natural and agricultural ecosystems is crucial for sustainable ecosystem management. This Special Issue aims to explore the functions of soil microorganisms in nutrient cycling and how they enhance the multifunctionality of ecosystems, providing fundamental and practical guidance for sustainable soil management. Potential topics of interest include the following:

  1. Microbial involvement in soil nutrient cycling.
  2. The diversity, community structure, and characteristics of key functional soil microorganisms and microbial food webs.
  3. Applications of soil microorganisms in vegetation restoration and agricultural production.
  4. The effects of global warming, nitrogen deposition, and agricultural management practices on soil microbial communities.
  5. Soil microorganisms in environmental remediation and soil erosion control. This Special Issue is open to the submission of fundamental, applied, and field research and review manuscripts on all aspects of these topics.

Dr. Dan Xiao
Dr. Yinhang Xia
Guest Editors

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 250 words) can be sent to the Editorial Office for assessment.

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. Microorganisms is an international peer-reviewed open access monthly 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

  • soil microbiome
  • nutrient cycling
  • soil micro-food web
  • land use change
  • ecosystem restoration
  • agricultural management

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Published Papers (5 papers)

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Research

21 pages, 6582 KB  
Article
Effects of Combined Application of Different Nitrogen Forms on Substrate Nutrient Utilization, Root Microenvironment, and Tomato Yield
by Shuyan Jiang, Jianhong Sun, Ning Jin, Shuya Wang, Shuchao Huang, Zhaozhuang Li, Jihua Yu, Jian Lyu and Li Jin
Microorganisms 2026, 14(1), 158; https://doi.org/10.3390/microorganisms14010158 - 10 Jan 2026
Viewed by 182
Abstract
In facility tomato production, the excessive application ratio of ammonium nitrogen (NH4+-N) often leads to root acidification and calcium-magnesium antagonism. Although amide nitrogen (urea-N) has better buffering properties, it needs to be hydrolyzed before utilization, resulting in a lag effect. [...] Read more.
In facility tomato production, the excessive application ratio of ammonium nitrogen (NH4+-N) often leads to root acidification and calcium-magnesium antagonism. Although amide nitrogen (urea-N) has better buffering properties, it needs to be hydrolyzed before utilization, resulting in a lag effect. Previous studies have mostly focused on a single nitrogen source or a fixed proportion, and there is still a lack of systematic evidence on the nitrogen supply effects of different nitrogen application combinations at different growth stages of tomatoes. Therefore, in this experiment, tomato cultivar ‘Jingfan 502’ was used. All treatments received the same total nitrogen concentration (15 mM), but the nitrogen was supplied as different combinations of ammonium nitrogen (AN) and amide nitrogen (UN). Six AN–UN ratio treatments were designed: CK (0% AN, 0% UN), T1 (100% AN, 0% UN), T2 (0% AN, 100% UN), T3 (25% AN, 75% UN), T4 (50% AN, 50% UN), and T5 (75% AN, 25% UN). T3 (25% NH4+ + 75% urea) increased single-plant yield by 64.04% and 5.10%, and total N, P, K, and Mg accumulation by 29.0% and 20.7%, relative to T1 and T2. In addition, compared to T1 and T2, the nitrogen fertilizer uptake rate of the T3 treatment increased by 17.00% and 24.90%, respectively, and the electrical conductivity (EC) increased by 27.04% and 44.84%, respectively. Redundancy Analysis (RDA) showed that enzyme activities, total N and electrical conductivity were positively linked to microbial communities in T3 and T4, whereas communities in CK, T1, T2 and T5 correlated with nutrients and pH. Under controlled pot conditions, T3 optimizes the rhizosphere micro-environment, enhances microbial abundance and nutrient uptake, and provides a theoretical basis for precise N management in tomato. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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21 pages, 6648 KB  
Article
Biochar Integrate with Beneficial Microorganisms Boosts Soil Organic Fractions by Raising Carbon-Related Enzymes and Microbial Activities in Coastal Saline-Alkali Land
by Rui Wang, Qian Cui, Zeyuan Wang, Hongjun Yang, Yuting Bai and Ling Meng
Microorganisms 2026, 14(1), 115; https://doi.org/10.3390/microorganisms14010115 - 5 Jan 2026
Viewed by 312
Abstract
Biochar and beneficial microorganisms (BM) is considered promising soil amendment for saline-alkali amelioration and soil carbon storage.However, the effects of biochar combined with BM addition soil organic carbon (SOC) accumulation and microbial characteristics are less known in coastal saline-alkali soil. Herein, we investigated [...] Read more.
Biochar and beneficial microorganisms (BM) is considered promising soil amendment for saline-alkali amelioration and soil carbon storage.However, the effects of biochar combined with BM addition soil organic carbon (SOC) accumulation and microbial characteristics are less known in coastal saline-alkali soil. Herein, we investigated the SOC content and fractions, soil carbon enzyme activities, and microbial community composition in coastal saline-alkali soil, following three levels of biochar and BM addition. Compared to the control treatment, biochar and BM application effectively reduced soil salinity by 37.58–66.53% and increased soil NH4+ by 9.49–121.16% and NO3− by 43.56–254.28%, respectively. Biochar integrated with BM addition significantly increased the content of SOC, soil mineral-associated organic carbon (MAOC), soil particulate organic carbon (POC), and carbon pool management index (CPMI) by 37.76–108.02%, 15.43–140.44%, 13.73–64.55%, and 81.11–154.61%, respectively, compared with CK treatment. Additionally, biochar and BM significantly enhanced the activities of soil carbon cycle enzymes, including α-1,4-glucosidase (14.54–124.45%), β-1,4-glucosidase (12.71–133.98%), and cellulose hydrolase (6.07–19.17%). Biochar and BM addition also improved the bacterial diversity and altered the microbial composition at the phylum level. The co-addition of biochar and BM improved SOC by decreasing soil salinity and, enhancing soil nutrient availability, soil carbon cycle enzymes, and microbial activity. Furthermore, the combination of 4% biochar and BM exhibited the highest MAOC/POC ratio, demonstrating the most significant impacts on enhancing SOC stability in coastal saline-alkali soil. This study highlighted that the combined use of biochar and BM could serve as a promising approach to fortify soil carbon pool content and stability in saline-alkali land. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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16 pages, 5196 KB  
Article
Spring Rest-Grazing Time Influenced Soil Phosphorus Fractions by Altering the Abundance of Genes Involved in Phosphorus Cycling in a Subalpine Meadow
by Hong Xiao, Yuanyuan Jing, Kai Ma, Yun Wang, Changlin Xu and Xiaojun Yu
Microorganisms 2025, 13(11), 2618; https://doi.org/10.3390/microorganisms13112618 - 18 Nov 2025
Viewed by 418
Abstract
Soil phosphorus (P) availability is a critical factor limiting plant growth and ecosystem productivity that can be strongly influenced by land use factors, such as grazing by livestock. Seasonal grazing management can benefit grassland productivity and soil nutrient cycling in alpine meadows, but [...] Read more.
Soil phosphorus (P) availability is a critical factor limiting plant growth and ecosystem productivity that can be strongly influenced by land use factors, such as grazing by livestock. Seasonal grazing management can benefit grassland productivity and soil nutrient cycling in alpine meadows, but its effects on soil P availability and the microbial processes driving P transformation remain poorly understood. To address this, a long-term field experiment was conducted with five different spring rest-grazing periods, where soil P fractions were examined and metagenomic sequencing was employed to assess the functional profiles of microbial genes involved in P cycling. Early spring rest-grazing led to higher concentrations of labile P fractions (Resin-P and NaHCO3-Pi), indicating improved soil P availability. Moreover, rest-grazing in early spring significantly reduced HCl-Pi concentration while increased the concentration of conc. HCl-Po. Metagenomic analysis revealed that early spring rest-grazing may have contributed to a higher relative abundance of the organic P mineralization gene phnA but decreasing the relative abundance of inorganic P solubilization genes ppa, and P-uptake and transport gene pstB. The dominant microbial genera involved in P cycling were Rhodopseudomonas and Mesorhizobium. Soil temperature and water infiltration rate, both affected by early rest-grazing, were identified as the main environmental variables correlated with P-cycling functional gene composition. These influenced taxa with functional genes involving organic P mineralization, inorganic P solubilization, and P-uptake and transport, which may associate with enhancing soil labile P. This study provides insights into potential microbial processes under grazing management in grassland ecosystems. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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20 pages, 5671 KB  
Article
Precipitation Alleviates Adverse Effects of Nitrogen and Phosphorus Enrichment on Soil Microbial Co-Occurrence Network Complexity and Stability in Karst Shrubland
by Jiangnan Li, Jie Zhao, Xionghui Liao, Xianwen Long, Wenyu Wang, Peilei Hu, Wei Zhang and Kelin Wang
Microorganisms 2025, 13(9), 2012; https://doi.org/10.3390/microorganisms13092012 - 28 Aug 2025
Cited by 1 | Viewed by 1010
Abstract
The karst region is highly ecologically fragile due to its unique geology and poor water and nutrient retention. Despite long-term restoration, vegetation often remains in the secondary shrubland stage. Soil microorganisms play a vital role in maintaining ecosystem functions, but how microbial communities [...] Read more.
The karst region is highly ecologically fragile due to its unique geology and poor water and nutrient retention. Despite long-term restoration, vegetation often remains in the secondary shrubland stage. Soil microorganisms play a vital role in maintaining ecosystem functions, but how microbial communities respond to combined water and nitrogen-phosphorus nutrient changes in karst shrubland remains poorly understood. This knowledge gap hinders effective restoration strategies in karst shrublands. Here, the effects of water, nitrogen, and phosphorous additions and their interactions on soil physico-chemical properties, soil microbial abundance, diversity, community composition, and the co-occurrence network were explored. A full factorial experiment (water × nitrogen × phosphorous, each at two levels) was conducted in a karst shrubland with over 20 years of vegetation restoration, with treatments including control, water (+120 mm yr−1), nitrogen (+20 g N m−2 yr−1), phosphorus (+16 g P m−2 yr−1), and their four combinations. Our results suggested that water addition significantly increased soil water content and soil microbial abundance but reduced fungal diversity. Nitrogen addition significantly increased soil nitrate nitrogen content and fungal diversity, and fungal diversity showed an increasing trend under phosphorous addition. The addition of nitrogen and phosphorous did not significantly alter the soil microbial community composition, while water addition showed a tendency to change the soil fungal community composition. Network topological properties, robustness, and vulnerability analyses indicated that individual nitrogen or phosphorous additions, as well as their interactions, reduced network complexity and stability. In contrast, water addition alone or in combination with nitrogen and/or phosphorous alleviated these negative effects, and the water and phosphorous interaction exhibited the highest levels of network complexity and stability. Further analysis showed that the soil pH, available phosphorous, ratio of carbon to phosphorous, and ammonium nitrogen were explanatory variables contributing significantly to soil microbial abundance, diversity, community composition, and network complexity. Overall, these findings highlighted the pivotal role of water availability in enhancing soil microbial stability under nutrient enrichment, offering valuable insights into ecological restoration in karst ecosystems. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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20 pages, 2743 KB  
Article
Systematic Investigation of Phosphate Decomposition and Soil Fertility Modulation by the Filamentous Fungus Talaromyces nanjingensis
by Xiao-Rui Sun, Pu-Sheng Li, Huan Qiao, Wei-Liang Kong, Ya-Hui Wang and Xiao-Qin Wu
Microorganisms 2025, 13(7), 1574; https://doi.org/10.3390/microorganisms13071574 - 3 Jul 2025
Cited by 1 | Viewed by 1011
Abstract
Phosphate-solubilizing microbes (PSMs) in soil play a crucial role in converting insoluble phosphates into plant-available soluble phosphorus. This paper systematically presents a comprehensive array of qualitative and quantitative techniques to assess the phosphate-decomposing capabilities of microbes. Additionally, it introduces two optimized media, namely [...] Read more.
Phosphate-solubilizing microbes (PSMs) in soil play a crucial role in converting insoluble phosphates into plant-available soluble phosphorus. This paper systematically presents a comprehensive array of qualitative and quantitative techniques to assess the phosphate-decomposing capabilities of microbes. Additionally, it introduces two optimized media, namely improved Monkina medium No. 1 and No. 2, which are particularly suitable for detecting the solubilization abilities of microbes toward insoluble organic phosphates. Talaromyces nanjingensis, a novel fungal species recently isolated from the rhizosphere soil of Pinus massoniana, demonstrates remarkable phosphate-solubilizing abilities. Across multiple temperature gradients (15 °C, 20 °C, 25 °C, 30 °C, and 37 °C), it effectively decomposes both insoluble inorganic and organic phosphates. This is achieved through the secretion of organic acids, including gluconic acid (6.10 g L−1), oxalic acid (0.93 g L−1), and malonic acid (0.17 g L−1), as well as phosphate-solubilizing enzymes. Moreover, under low-, medium-, and high-temperature conditions, T. nanjingensis can decompose insoluble phosphates in three types of soil with varying pH levels, thereby enhancing the overall soil fertility. Genomic analysis of T. nanjingensis has identified approximately 308 genes associated with phosphate decomposition and environmental adaptability, validating its superior capabilities and multi-faceted strategies for phosphate mobilization. These findings underscore the wide applicability of T. nanjingensis in maintaining soil phosphorus homeostasis and optimizing the phosphorus use efficiency, highlighting its promising potential for agricultural and environmental applications. Full article
(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)
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