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Microorganisms
Special Issues
Microbial Mechanisms for Soil Improvement and Plant Growth
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Microbial Mechanisms for Soil Improvement and Plant Growth

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 28 February 2026 | Viewed by 3908

Special Issue Editors

Dr. Qicong Wu

E-Mail Website
Guest Editor
Co-Innovation Center for Soil-Water and Forest-Grass Ecological Conservation in Yellow River Basin of Shandong Higher Education Institutions, College of Forestry, Shandong Agricultural University, Tai’an 271018, China
Interests: soil science; microorganisms; agronomy; environmental science; climate change
Dr. Hui Zhang

E-Mail Website
Guest Editor
Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014,China
Interests: soil science; improvement and utilization of saline-alkali soil; soil microorganisms; agronomy

Special Issue Information

Dear Colleagues,

Microorganisms show strong adaptability under different environmental stresses. By changing the physical and chemical characteristics of soil, they improve soil structure, accelerate nutrient turnover, promote the accumulation of soil organic carbon, and create a more favorable growth environment for plants. The Special Issue aims to investigate the pivotal role of microorganisms in shaping soil ecosystems and enhancing plant growth under various environmental stresses, such as extreme temperatures, water deficits, waterlogging, saline-alkali conditions, and nutrient limitations. 

We invite contributions that analyze the physiological and biochemical responses of microbial communities to these stressors and how such adaptations can modify soil properties, nutrient cycling, and overall soil health. Furthermore, articles that explore how these microbial changes create a beneficial environment for plant growth, including the enhancement of nutrient availability, improvements in soil structure, etc., are also welcome. 

By integrating experimental research, field studies, and theoretical models, this Special Issue aims to provide a comprehensive understanding of the interactions between microorganisms and their soil environment. We aim to highlight the mechanisms through which microbes not only withstand environmental pressures but also contribute to sustainable agricultural practices and ecosystem resilience. We welcome innovative studies that explore these critical dynamics in the context of climate change.

Dr. Qicong Wu
Dr. Hui Zhang
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

  • microbial adaptation
  • soil health
  • environmental stresses
  • plant growth promotion
  • nutrient cycling

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Published Papers (4 papers)

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Research

17 pages, 1988 KB  
Article
Synergistic Application of Humic Acid and Microbial Fertilizers Improve Soil Quality, Reshape Microbial Network, and Enhance Wheat Yield in Coastal Saline–Alkali Soils
by Lei Ma, Yudong Li, Yufeng Zhang, Yan Li, Jianlin Wei, Zhaohui Liu and Deshui Tan
Microorganisms 2025, 13(12), 2716; https://doi.org/10.3390/microorganisms13122716 - 28 Nov 2025
Viewed by 353
Abstract
Coastal saline–alkali soils represent one of the most challenging agroecosystems due to coupled chemical, physical, and biological constraints. Although humic acid (HA) and microbial fertilizers (MFs) are recognized as effective amendments, the mechanisms linking soil improvements to yield gains remain unclear. Here, a [...] Read more.
Coastal saline–alkali soils represent one of the most challenging agroecosystems due to coupled chemical, physical, and biological constraints. Although humic acid (HA) and microbial fertilizers (MFs) are recognized as effective amendments, the mechanisms linking soil improvements to yield gains remain unclear. Here, a 2-year field experiment was conducted in the Yellow River Delta to assess the effects of HA, applied alone or in combination with Bacillus subtilis and Trichoderma harzianum, on soil salinity, nutrient availability, aggregate stability, microbial communities, and wheat yields. Results showed that HA application alone reduced soil electrical conductivity (EC) and total soluble salts (TSS), and enhanced aggregate mean weight diameter (MWD), leading to 40.94–55.64% higher yields. Co-application with MFs further amplified these improvements, lowering EC and TSS up to 77.04% and 73.83%, enhancing MWD by 122.50%, and raising yields by 75.79%. Soil enzyme activities (e.g., catalase, β-glucosidase, urease, and alkaline phosphatase) and fungal diversity were substantially enhanced, whereas bacterial diversity showed no significant change. Co-occurrence network analysis demonstrated that application of HA with MFs (particularly with B. subtilis) reshaped microbial networks by enriching modules linked to nutrient provisioning, aggregate stability, and enzyme activity, while suppressing modules associated with salinity tolerance. Keystone species such as Lysobacter and Massilia were significantly enriched and closely associated with soil chemical and aggregate improvements. Structural equation modeling further revealed that yield gains were mainly explained by reduced salinity and enhanced aggregate stability rather than nutrient provisioning. These findings provide mechanistic evidence that HA improves soil quality and wheat productivity in coastal saline–alkali soils through integrated chemical, physical, and biological pathways, and that these benefits are strengthened when combined with microbial fertilizers. Full article
(This article belongs to the Special Issue Microbial Mechanisms for Soil Improvement and Plant Growth)
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19 pages, 3229 KB  
Article
Reduced Chemical Fertilizer Combined with Organic Fertilizer Alters the Soil Microbial Community and Enhances Soil Microbial Diversity of Acanthopanax senticosus Cultivation
by Zhuolun Li, Xin Sui, Mengsha Li, Zhimin Yu, Pin Lv, Limin Wang, Jizhou Zhang and Wenqi Li
Microorganisms 2025, 13(12), 2709; https://doi.org/10.3390/microorganisms13122709 - 27 Nov 2025
Viewed by 334
Abstract
To investigate the response of soil microbial communities to reduce chemical fertilization supplementation with organic fertilizer in Acanthopanax senticosus cultivation, we analyzed the diversity, composition, and structure of soil microbiota by using high-throughput sequencing technology. The results showed that reducing chemical fertilizer application [...] Read more.
To investigate the response of soil microbial communities to reduce chemical fertilization supplementation with organic fertilizer in Acanthopanax senticosus cultivation, we analyzed the diversity, composition, and structure of soil microbiota by using high-throughput sequencing technology. The results showed that reducing chemical fertilizer application significantly increased soil microbial richness (ACE and Chao1 indices), which was positively correlated with soil total nitrogen (TN) content. At the phylum level, the relative abundance of Cyanobacteria decreased at T2 (reduction of 20% for fertilizer application) but increased at T4 (reduction of 60% for fertilization application), exhibiting an opposite trend to Bacteroidetes. At the genus level, the relative abundance of Paucibacter was significantly higher in T4 than in other treatments, while Nitrospira reached its peak under T3 treatment. For fungal communities, the richness index showed a non-linear response, initially decreasing and then increasing, which was positively correlated with the soil available potassium (AK) content. At the phylum level, reduced fertilizer application significantly reduced the relative abundance of Ascomycota compared to conventional fertilization. At the genus level, the relative abundance of Fusarium was significantly lower in the T4 treatment than in the other treatments. Redundancy analysis (RDA) revealed that the total organic carbon (TOC), TN, and AK were the key environmental factors affecting the soil microbial community. This study demonstrated that partial substitution of chemical fertilizers with organic amendments can improve soil physicochemical properties and enhance microbial diversity, providing a scientific basis for developing sustainable fertilization strategies for Acanthopanax senticosus cultivation. Full article
(This article belongs to the Special Issue Microbial Mechanisms for Soil Improvement and Plant Growth)
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20 pages, 3025 KB  
Article
Variations in the Structure and Composition of Soil Microbial Communities of Different Forests in the Daxing’anling Mountains, Northeastern China
by Han Qu, Mingyu Wang, Xiangyu Meng, Youjia Zhang, Xin Gao, Yuhe Zhang, Xin Sui and Maihe Li
Microorganisms 2025, 13(6), 1298; https://doi.org/10.3390/microorganisms13061298 - 3 Jun 2025
Cited by 2 | Viewed by 1169
Abstract
Soil microorganisms are crucial in global biogeochemical cycles, impacting ecosystems’ energy flows and material cycling. This study, via high-throughput sequencing in four forests—the original Larix gmelinii (Rupr.) Kuzen. forest (LG), the conifer–broad-leaved mixed Pinus sylvestris var. mongolica Litv. forest (PS), the original pure [...] Read more.
Soil microorganisms are crucial in global biogeochemical cycles, impacting ecosystems’ energy flows and material cycling. This study, via high-throughput sequencing in four forests—the original Larix gmelinii (Rupr.) Kuzen. forest (LG), the conifer–broad-leaved mixed Pinus sylvestris var. mongolica Litv. forest (PS), the original pure Betula platyphylla Sukaczev forest (BP), and the original pure Populus L. forest (PL) in Shuanghe National Nature Reserve, Daxing’anling mountains—explored soil microbial community structures and diversities. The results indicated that the BP and PL forests had the lowest soil bacterial ACE and Chao1 indices, and the original pure birch forest’s Shannon index was higher than that of the poplar forest. The soil’s fungal Chao1 index of the birch forest was higher than that of the larch forests. Bradyrhizobium and Roseiarcus were the dominant soil bacterial genera; the dominant soil fungal genera were Podila, Russula, and Sebacina. RDA and mantel analyses indicated that soil microbial community structures varied across forest types mainly because of the effective phosphorous and pH levels, soil’s total nitrogen level, and available phosphorus level. This study offers a scientific foundation for cold-temperate-forest ecosystem management regarding soil microbial diversity and community structural changes in different forest types. Full article
(This article belongs to the Special Issue Microbial Mechanisms for Soil Improvement and Plant Growth)
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12 pages, 1583 KB  
Article
Jet-Breaking Extrusion of Alginate–Chitosan Capsules for Encapsulation of Plant Growth–Promoting Extremophilic Fungi
by César Arriagada-Escamilla, Javier Ortiz, Nicole Iturra, Javiera Soto and Eduardo Morales
Microorganisms 2025, 13(5), 1123; https://doi.org/10.3390/microorganisms13051123 - 14 May 2025
Cited by 1 | Viewed by 1485
Abstract
Drought and metal pollution severely impact plant growth. Root-associated extremophilic fungi can improve plant performance, and their encapsulation improves protection and effectiveness. This study optimized the encapsulation conditions for an extremophilic fungus with plant growth-promoting traits using alginate–chitosan capsules. An endophytic fungus was [...] Read more.
Drought and metal pollution severely impact plant growth. Root-associated extremophilic fungi can improve plant performance, and their encapsulation improves protection and effectiveness. This study optimized the encapsulation conditions for an extremophilic fungus with plant growth-promoting traits using alginate–chitosan capsules. An endophytic fungus was isolated from the roots of Neltuma chilensis from the Atacama Desert and identified via internal transcribed spacer (ITS) sequencing. Its plant growth-promoting traits, including exopolysaccharide, ammonium, siderophore, and indole acetic acid production and phosphorus solubilization, were evaluated. Freeze-dried Penicillium nalgiovense was encapsulated using jet-breaking extrusion, and capsule morphology and fungal survival were assessed via scanning electron microscope (SEM), confocal laser scanning microscopy (CLSM), and viability tests. Using Taguchi’s design, optimal conditions for sphericity (0.914 ± 0.002) and mean size (3.232 ± 0.087 mm) were achieved with 1% chitosan, a 5 cm distance to the gelation bath, and a 40 Hz vibration frequency. CLSM analysis confirmed the presence of the chitosan outer layer, revealing the capsule’s coating material encapsulating the fungus P. nalgiovense. The encapsulated fungus remained viable across disinfection times, demonstrating effective protection and gradual release. These findings emphasize the need for precise parameter control in fungal encapsulation, providing a basis for developing robust bioinoculants to support plant resilience in extreme environments. Full article
(This article belongs to the Special Issue Microbial Mechanisms for Soil Improvement and Plant Growth)
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