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Microorganisms
Special Issues
Advances in Soil Microbial Ecology, 4th Edition
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Advances in Soil Microbial Ecology, 4th Edition

A Special Issue of Microorganisms (ISSN 2076-2607) belonging to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 1747

Editors

Dr. Jie Wang

E-Mail Website
Guest Editor
Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China
Interests: plant-soil-microbe interaction; soil microbiology; restoration ecology; land use change; soil carbon; vegetation restoration; soil conversation; global change; soil phosphorus
Special Issues, Collections and Topics in MDPI journals
Dr. Yadong Xu

E-Mail Website
Guest Editor
School of Agriculture and Biomanufacturing, Zhengzhou University, Zhengzhou 450001, China
Interests: soil nitrogen cycle; soil microecology; stoichiometric ratio; community diversity; ccommunity assembly processes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil, a complex and dynamic ecosystem, harbors an incredibly diverse and intricate community of microorganisms that play fundamental roles in nutrient cycling, organic matter decomposition, and overall ecosystem functioning. The study of soil microbial ecology offers insights into the interactions between microorganisms and their environment, shedding light on the intricate web of life beneath our feet. This Special Issue aims to delve into the multifaceted realm of soil microbial ecology, exploring the interactions, functions, and adaptations of soil microorganisms that collectively shape terrestrial ecosystems.

The Special Issue invites the submission of original research articles, reviews, and perspectives that span a wide spectrum of topics within soil microbial ecology, including the following:

  • Microbial diversity and community structure in different soil types and ecosystems;
  • Microbial interactions and their roles in nutrient cycling and organic matter decomposition;
  • Responses of soil microbial communities to environmental changes and disturbances;
  • Microbial contributions to soil carbon and nitrogen dynamics;
  • Role of soil microorganisms in ecosystem resilience and restoration;
  • Advances in molecular techniques for studying soil microbial communities;
  • Microbial contributions to soil ecosystem services and sustainable agriculture.

Dr. Jie Wang
Dr. Yadong Xu
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-anonymized 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 microorganisms
  • microbial ecology
  • microbial community
  • microbial diversity
  • microbial interactions
  • soil ecosystem
  • nutrient cycle

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Related Special Issues

Published Papers (5 papers)

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Research

18 pages, 6441 KB  
Article
Spatial Variation in Mycosphere Soil Bacterial Communities of Leucopaxillus giganteus and Its Environmental Drivers in Shanxi, China
by Zhen Li, Ruixuan Wu, Mingqin Luo, Yang Xiao and Fei Yu
Microorganisms 2026, 14(9), 2029; https://doi.org/10.3390/microorganisms14092029 - 11 Sep 2026
Viewed by 217
Abstract
Leucopaxillus giganteus, a wild saprotrophic fungus with high edible and medicinal value, has not yet achieved large-scale artificial cultivation. To elucidate the abiotic and biotic factors governing its growth, we analyzed physicochemical properties and bacterial communities of mycosphere and bulk soils from [...] Read more.
Leucopaxillus giganteus, a wild saprotrophic fungus with high edible and medicinal value, has not yet achieved large-scale artificial cultivation. To elucidate the abiotic and biotic factors governing its growth, we analyzed physicochemical properties and bacterial communities of mycosphere and bulk soils from Shanxi Province, China. We observed geographic variation in the diversity, composition, and functional profiles of dominant mycosphere soil bacterial communities. Soil organic carbon, available potassium, altitude, longitude, and latitude were the key factors affecting mycosphere soil bacterial community structure. Distance–decay analysis revealed that the beta diversity of mycosphere soil bacterial communities declined with increasing geographical distance. Bacterial diversity in the L. giganteus mycosphere was significantly lower than that in bulk soil. Genera such as Micromonospora, Streptosporangium, Paraburkholderia, Pedobacter, Caballeronia, Paenibacillus, and Flavobacterium could act as saprotrophic helper bacteria in the mycosphere of L. giganteus. LEfSe analysis revealed 72 genera that exhibited significant abundance differences among samples from six geographic regions, including Bradyrhizobium, Sphingomicrobium, and Phyllobacterium. Functional annotation detected enriched pathways for transport and catabolism, signal transduction, and carbohydrate and lipid metabolism in mycosphere soil bacterial communities. These results advance our understanding of the ecological interactions of L. giganteus and support its artificial cultivation and sustainable resource use. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 4th Edition)
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18 pages, 5726 KB  
Article
Long-Term Organic Fertilization Drives Soil Organic Carbon Accumulation in Black Soil Through Microbial Necromass Carbon and CAZyme-Mediated Carbon Turnover
by Yang Liu, Haoyan Li, Xinxin Guo, Nan Wang, Ning Huang, Hongbin Wang, Jinhua Liu, Chenyu Zhao, Luze Yang, Biao Sui and Xingmin Zhao
Microorganisms 2026, 14(9), 1970; https://doi.org/10.3390/microorganisms14091970 - 7 Sep 2026
Viewed by 270
Abstract
Long-term organic inputs increase soil organic carbon (SOC) in black soil; however, it remains uncertain if straw and manure enhance SOC via separate microbial necromass carbon (MNC) routes. Therefore, a 12-year field experiment was conducted to explore this mechanism. Treatments included inorganic fertilizer, [...] Read more.
Long-term organic inputs increase soil organic carbon (SOC) in black soil; however, it remains uncertain if straw and manure enhance SOC via separate microbial necromass carbon (MNC) routes. Therefore, a 12-year field experiment was conducted to explore this mechanism. Treatments included inorganic fertilizer, partial substitution of inorganic fertilizer with straw, and partial substitution of inorganic fertilizer with manure, along with a no-fertilizer control. According to the results, compared with inorganic fertilizer alone, treatments involving both organic manure and straw returned markedly raised the levels of SOC, MNC, bacterial necromass carbon (BNC), and fungal necromass carbon (FNC). Notably, compared to the CK treatment, N75S showed a greater contribution of MNC to SOC (MNC/SOC), but in both N75M and M, the MNC/SOC was lower than in CK. The CAZyme genes related to hemicellulose, lignin, chitin, and peptidoglycan differed among treatments. Elevated gene abundances for plant-derived lignin and hemicellulose decomposition were observed under M and N75M, whereas they reduced the genes responsible for peptidoglycan and glucan. However, under N75S, there was a notable rise in the number of genes responsible for hemicellulose and lignin, as well as an increase in genes that degrade chitin and peptidoglycans. In conclusion, this finding demonstrates that long-term straw return tends to promote SOC stabilization primarily through the microbial necromass pathway, while the application of manure over the long term tends to increase the total SOC primarily through the input of exogenous organic carbon. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 4th Edition)
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16 pages, 4225 KB  
Article
Biochar-Associated Shifts in Nitrogen Status, Microbial Communities and Dissolved Organic Matter in Salt-Affected Maize Soil
by Rui Li, Chi Zhang, Yu Miao, Fangze Li, Ge Zhang, Qiwei Sun, Tianci Hua, Zhikun Pang and Xingjie Lin
Microorganisms 2026, 14(9), 1907; https://doi.org/10.3390/microorganisms14091907 - 28 Aug 2026
Viewed by 282
Abstract
Salt-affected soil constrains maize establishment, and rhizosphere and non-rhizosphere responses to soil biochar remain difficult to establish. We evaluated soil physical and nitrogen properties, qPCR marker genes, 16S and ITS communities, and molecular profiles of dissolved organic matter (DOM) in a 90-day randomized [...] Read more.
Salt-affected soil constrains maize establishment, and rhizosphere and non-rhizosphere responses to soil biochar remain difficult to establish. We evaluated soil physical and nitrogen properties, qPCR marker genes, 16S and ITS communities, and molecular profiles of dissolved organic matter (DOM) in a 90-day randomized complete block pot experiment (four biochar rates; five blocks; 20 pots). Control maize did not survive; control pots therefore yielded only non-rhizosphere soil, whereas rhizosphere and non-rhizosphere samples from biochar pots were paired. Block-adjusted comparisons showed higher water content and porosity and lower bulk density in all biochar non-rhizosphere groups than in the control (Holm-adjusted p < 0.05). Biochar-associated shifts in mineral-N partitioning and selected DNA-level marker-gene abundances accompanied design-aware community differences for NR treatment, R dose and pooled compartment (16S R2 = 0.360, 0.435 and 0.218; ITS R2 = 0.720, 0.712 and 0.304; all p < 0.001); fungal differences also included heterogeneous dispersion. D90 FT-ICR MS profiles described relative DOM molecular variation, but cross-layer residual associations did not survive false-discovery rate correction. Thus, biochar-associated physical and nitrogen changes coincided with microbial and relative DOM restructuring under the tested pot conditions. Because control survival was confounded with treatment, these are observed-group associations rather than pure causal biochar effects. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 4th Edition)
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18 pages, 1634 KB  
Article
Biochar and Bioorganic Fertilizer Amendment Improved Soil Qualities and Altered Bacterial Communities in Quinoa Rhizosphere Soils of the Yellow River Delta
by Meng Li, Yinyu Gu, Chuanjie Chen, Zongshuai Wang, Xiaohong Guo, Xiaoyan Liang, Kuihua Yi, Junlin Li, Dongyang Li and Haiyang Zhang
Microorganisms 2026, 14(9), 1878; https://doi.org/10.3390/microorganisms14091878 - 24 Aug 2026
Viewed by 262
Abstract
The application of biochar and bioorganic fertilizer (BOF) in agricultural systems has garnered increasing attention in recent years. Nevertheless, research remains scarce on the impacts of biochar and BOF on the rhizosphere microecological characteristics of saline-alkali soils. This research involved the execution and [...] Read more.
The application of biochar and bioorganic fertilizer (BOF) in agricultural systems has garnered increasing attention in recent years. Nevertheless, research remains scarce on the impacts of biochar and BOF on the rhizosphere microecological characteristics of saline-alkali soils. This research involved the execution and analysis of 16S rRNA sequencing using Illumina technology to explore how biochar, whether used alone or in conjunction with BOF, along with varying application rates, impacts the microbial community in the saline-alkali rhizosphere soil during quinoa cultivation. In the conducted field trial, sole BOF application, sole biochar application, and their combined application (referred to as BOFB) led to a substantial enhancement of 23.88%, 74.08–97.00%, and 188.88–220.59% in quinoa aerial biomass, respectively. Meanwhile, sole biochar application or biochar combined with BOF reduced soil electrical conductivity (EC) by 26.42–39.81%. Biochar and BOF significantly improved most soil parameters, with the exception of total phosphorus (TP). In comparison to the control (CK), the relative abundances of Pseudomonas, Arthrobacter, Skermanella, and Bacillus were elevated in the biochar and BOFB treatments, while Sphingomonas was more abundant in the BOF treatment. In addition, Skermanella exhibited a significant positive correlation with EC and available potassium (AK). Biochar exerted a stronger effect on soil bacterial community structure than BOF. Furthermore, the complexity of the bacterial community in biochar and BOFB treatments far exceeded that in the BOF and CK treatments. Overall, the application of biochar effectively reduced soil EC and improved soil fertility, enhanced bacterial community stability, and optimized bacterial community structure, thereby increasing quinoa aerial biomass. Under the conditions of this study, the optimal application rate for biochar was 15 t/ha, and the combined application of biochar and BOF produced superior effects relative to either amendment alone. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 4th Edition)
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25 pages, 17395 KB  
Article
Mechanisms of 915 MHz Microwave Thermal Treatment on Physicochemical Properties and Microbial Communities in Sugarcane Continuous Cropping Soil
by Junru Mao, Yanling Wu, Yifeng Huang, Yunyun Li, Min Mo, Yanye Fan, Xianrui Chen and Zhimin Huang
Microorganisms 2026, 14(8), 1831; https://doi.org/10.3390/microorganisms14081831 - 19 Aug 2026
Viewed by 490
Abstract
Long-term sugarcane monoculture triggers severe continuous cropping obstacles accompanied by notable soil microecological degradation, including nutrient immobilization, soil acidification, salinization and microbial community imbalance. Physical soil remediation via industrial microwave irradiation represents a promising approach to alleviate soil degradation. Nevertheless, the interactive variations [...] Read more.
Long-term sugarcane monoculture triggers severe continuous cropping obstacles accompanied by notable soil microecological degradation, including nutrient immobilization, soil acidification, salinization and microbial community imbalance. Physical soil remediation via industrial microwave irradiation represents a promising approach to alleviate soil degradation. Nevertheless, the interactive variations in soil structure, fertility and microbial communities under gradient 915 MHz industrial microwave irradiation remain poorly understood. This study aimed to clarify the correlations among physicochemical properties, microbial structure and functional genes of sugarcane continuous cropping soil under microwave thermal regulation. A continuous 915 MHz microwave device with power gradients (0, 2, 4, 6, 8 kW) and a fixed irradiation duration of 10 min was adopted. Soil samples were incubated for 0, 15 and 30 weeks for comprehensive parameter determination. The results demonstrated that appropriate microwave power exerted positive regulatory effects on soil thermal intensity, aggregate disruption and microbial succession. Soil organic matter (SOM) and pH were key factors modulating the distribution of beneficial and pathogenic microorganisms. The 4 kW treatment disintegrated compact soil aggregates, activated mineral-bound nutrients, relieved soil acidification and salinization, and upregulated genes responsible for nutrient mineralization and antifungal metabolism to sustain high abundances of partial biocontrol fungi. In contrast, high-power treatments (6 kW and 8 kW) induced substantial early-stage SOM loss, reduced soil pH and aggravated salinization in the late incubation stage, thereby inhibiting symbiotic beneficial fungi. Collectively, 4 kW was the optimal microwave parameter in this study to coordinate soil structural, nutritional and microecological balance. This study provides a theoretical basis and technical guidance for the green remediation of soil plagued by sugarcane continuous cropping obstacles. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 4th Edition)
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