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Microorganisms
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Advances in Soil Microbial Ecology, 3rd Edition
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Advances in Soil Microbial Ecology, 3rd Edition

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

Deadline for manuscript submissions: closed (30 April 2026) | Viewed by 5994

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 Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
Interests: soil nitrogen cycle; soil microecology; stoichiometric ratio; community diversity; community 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, decomposition of organic matter, 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:

  • 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 (8 papers)

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Research

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21 pages, 3954 KB  
Article
Microbial Necromass and Extracellular Enzyme Activities Are Associated with Depth-Dependent Soil Carbon Stabilization Along a Wildfire-Severity Gradient
by Shaqian Liu and Rui Yang
Microorganisms 2026, 14(6), 1380; https://doi.org/10.3390/microorganisms14061380 (registering DOI) - 22 Jun 2026
Abstract
Wildfire can alter soil organic carbon (SOC) pools and microbial pathways of carbon stabilization, but depth-dependent links between microbial necromass and stable carbon pools remain unclear. We investigated a wildfire-severity gradient in a subtropical coniferous forest in Guizhou, China, including four severity classes [...] Read more.
Wildfire can alter soil organic carbon (SOC) pools and microbial pathways of carbon stabilization, but depth-dependent links between microbial necromass and stable carbon pools remain unclear. We investigated a wildfire-severity gradient in a subtropical coniferous forest in Guizhou, China, including four severity classes (unburned, light, moderate, and severe) and two soil layers (0–20 and 20–40 cm). We measured easily oxidizable organic carbon (EOC), recalcitrant organic carbon (ROC), SOC, amino sugars, microbial necromass carbon (MNC), extracellular enzyme activities, and carbohydrate-active enzyme (CAZy) functional indices. MNC peaked under moderate wildfire in both layers, increasing by 73.8% and 85.1% in the topsoil and subsoil, respectively, relative to unburned plots. After accounting for soil physicochemical properties and wildfire severity, MNC was more strongly associated with ROC and SOC in the topsoil than in the subsoil. Extracellular enzyme activities were positively associated with amino sugars and necromass pools, whereas CAZy composite indices showed weaker relationships that did not persist after false discovery rate correction. Exploratory path analysis suggested that the EOC–NAG–MNC–ROC–SOC chain was more pronounced in the topsoil, while the subsoil showed weaker chained associations and stronger direct EOC–MNC and EOC–ROC links. Overall, microbial necromass was associated with depth-dependent post-fire carbon stabilization. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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21 pages, 8988 KB  
Article
Soil Fungal Community Dynamics Are More Strongly Influenced by Crop Growth Stage than by Straw Retention Amount Under Long-Term Wheat–Soybean Rotation
by Dejie Kong, Nana Liu, Yajing Guan, Chengjie Ren, Jiao Sun, Chengjin Guo, Guangxin Ren and Yongzhong Feng
Microorganisms 2026, 14(6), 1249; https://doi.org/10.3390/microorganisms14061249 - 2 Jun 2026
Viewed by 344
Abstract
Although soil fungi play a crucial role in straw decomposition, mineralization, nutrient cycling, and soil fertility, soil nitrogen and carbon stoichiometry across crop growth stages under long-term straw retention and wheat–soybean rotation remains poorly understood. We assessed the dynamic changes in soil fungal [...] Read more.
Although soil fungi play a crucial role in straw decomposition, mineralization, nutrient cycling, and soil fertility, soil nitrogen and carbon stoichiometry across crop growth stages under long-term straw retention and wheat–soybean rotation remains poorly understood. We assessed the dynamic changes in soil fungal communities under no straw (NS) retention, half straw (HS) retention, and total straw (TS) retention in winter wheat and summer soybean rotation. Compared with the NS treatment, average total nitrogen (TN) increased by 11.86% and 17.71% and mean soil organic carbon (SOC) increased by 4.10% and 13.08% under the HS and TS treatments, respectively. NO3−-N/TN and microbial biomass nitrogen (MBN)/TN ratios increased with the increase in straw retention; NH4+-N/TN and dissolved organic carbon/SOC ratios decreased. Microbial biomass carbon (MBC)/SOC increased and subsequently decreased as straw retention increased. The mean soil C:N ratio increased, and the MBC/MBN ratio decreased as straw retention increased. Crop growth stage and straw retention treatments significantly influenced soil fungal diversity and abundance; while they did not induce changes in the dominant species, they affected relative abundance. Soil fungal relative abundance and community dynamics were more sensitive to crop growth than to straw retention treatments. Mantel’s r statistic and Pearson correlation coefficient suggest that soil chemical stoichiometric ratios are useful indicators of relationships among the fungal community, soil nutrient status, and crop cultivation. Therefore, straw retention may be suitable for long-term wheat–soybean rotation. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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29 pages, 146751 KB  
Article
Network Topology and Undominated Assembly Processes Govern Soil Nematode Community Responses to Forest Type
by Bing Yang, Zhihe Zhang, Yue Liu, Zhidi Wang, Yuanlan Sheng and Zhisong Yang
Microorganisms 2026, 14(5), 1147; https://doi.org/10.3390/microorganisms14051147 - 19 May 2026
Viewed by 347
Abstract
Soil nematodes are integral to soil micro-food webs and serve as sensitive bioindicators of soil ecological condition. However, how forest vegetation and soil properties interact to shape nematode community assembly, network structure, and functional stability remains inadequately understood. Using 18S rRNA gene amplicon [...] Read more.
Soil nematodes are integral to soil micro-food webs and serve as sensitive bioindicators of soil ecological condition. However, how forest vegetation and soil properties interact to shape nematode community assembly, network structure, and functional stability remains inadequately understood. Using 18S rRNA gene amplicon sequencing coupled with phylogenetic null modeling, we examined soil nematode communities across four forest types along a succession gradient. Although taxonomic diversity (e.g., Shannon and Pielou indices) differed significantly among forest types, network topology and stochastic assembly processes were more closely associated with community restructuring and co-occurrence patterns. This suggests that, while diversity is not irrelevant, network- and assembly-based metrics provide complementary and often more sensitive indicators of nematode community responses to forest type. Co-occurrence network analysis revealed that mixed forests fostered more complex and potentially stable networks, whereas plantations formed dense but potentially vulnerable networks. Assembly processes were not dominated by strong deterministic selection (|βNTI| ≤ 2 for most comparisons), a pattern consistent with undominated processes (e.g., ecological drift, weak environmental filtering). Dispersal limitation played a negligible role in this system. Partial Least Square Path Modeling identified spatial factors and key soil properties (e.g., pH, electrical conductivity, soil water content, and organic carbon) as primary drivers of community structure. Our findings indicate that assessing soil food web health should integrate network analysis and stochasticity metrics rather than rely solely on taxonomic diversity. For sustainable forest management, mixed-species stands are preferable to monoculture plantations, and maintaining soil physicochemical heterogeneity is critical for community stability. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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23 pages, 3645 KB  
Article
Soil Microbial Diversity and Its Environmental Drivers in the Rhizosphere Profile of Camellia reticulata
by Fu-Jun Yan, Chong Ma, Hong-Xing Xiao, Yu-Jia Zeng, Yuan-Yuan Huang, Zhi-Yu Zhang, Zhong-Lang Wang, Long-Qing Chen and Fang Geng
Microorganisms 2026, 14(4), 806; https://doi.org/10.3390/microorganisms14040806 - 1 Apr 2026
Viewed by 484
Abstract
To investigate the main drivers of rhizosphere soil microbial community structure and diversity in Camellia reticulata, this study collected rhizosphere soil samples from six regions at two soil depths (0–30 cm and 30–60 cm). Using high-throughput sequencing, we systematically analyzed the effects [...] Read more.
To investigate the main drivers of rhizosphere soil microbial community structure and diversity in Camellia reticulata, this study collected rhizosphere soil samples from six regions at two soil depths (0–30 cm and 30–60 cm). Using high-throughput sequencing, we systematically analyzed the effects of soil environmental factors on microbial communities. The results showed that the dominant bacterial phyla were Proteobacteria, Acidobacteriota, Chloroflexi, Actinobacteriota, and Bacteroidota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. Alpha diversity of both bacterial and fungal communities was higher in surface soils (0–30 cm) than in deeper layers (30–60 cm), although the differences were not statistically significant (p > 0.05). Soil pH, potassium content (K), and catalase activity (S-CAT) were identified as the main environmental factors significantly correlated with microbial community structure. Network analysis identified Acidobacteriota and Ascomycota as highly connected taxa within microbial networks, suggesting their potential importance in maintaining network structure. This study reveals the vertical differentiation characteristics of rhizosphere microbial communities in C. reticulata and their responses to environmental factors, providing a theoretical basis for cultivation management and rhizosphere microecological regulation. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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15 pages, 2190 KB  
Article
Diversity and Community Structure of Soil Bacteria of Different Vegetation Types in Volcanic Lava of Wudalianchi, China
by Jiahui Cheng, Lihong Xie, Mingyue Jiang, Hongjie Cao, Fan Yang and Qingyang Huang
Microorganisms 2026, 14(3), 666; https://doi.org/10.3390/microorganisms14030666 - 15 Mar 2026
Viewed by 613
Abstract
Volcanic lava has a complete primary succession; the plant community composition can explain a great part of the variation of soil microbial diversity and community structure. Bacteria dominate the soil microbial communities in abundance and diversity, and they are important drivers of organic [...] Read more.
Volcanic lava has a complete primary succession; the plant community composition can explain a great part of the variation of soil microbial diversity and community structure. Bacteria dominate the soil microbial communities in abundance and diversity, and they are important drivers of organic matter decomposition and nutrient cycling. With 16S rRNA Illumina Miseq sequencing techniques, we analyzed the soil bacterial communities and diversities associated with different vegetation types in Wudalianchi. Shrub soils had the highest pH, MC, TOC, TN, AP, AN and NN, whereas moss soils had the lowest. The Shannon, Ace, and Pd indices of bacteria showed significant differences in the different vegetation types (p < 0.05). Bacterial Ace, Shannon, and Simpson indices peaked in Herb and Shrub is highest. The Proteobacteria, Actinobacteriota, Acidobacteriota, Planctomycetota and Chloroflexota were the most abundant groups at phyla level. Bacterial community composition varied significantly across vegetation types (p < 0.05). At the family level, Pseudonocardiaceae predominated in moss soils. Redundancy analysis and correlation analysis revealed MC, pH, and TP as key environmental factors shaping bacterial communities. Functional predictions based on taxonomic data indicated that chemoheterotrophy and aerobic chemoheterotrophy were the predominant functional groups. In conclusion, although soil microbial composition and diversity differed markedly across vegetation types following volcanic eruptions, functional groups prioritized carbon fixation strategies. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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13 pages, 1635 KB  
Article
Soil Microbial Life History Strategies Drive Microbial Carbon Use Efficiency Following Afforestation
by Hongyan Cheng, Haoyuan Chong, Minshu Yuan, Chengjie Ren, Jun Wang and Fazhu Zhao
Microorganisms 2025, 13(12), 2870; https://doi.org/10.3390/microorganisms13122870 - 17 Dec 2025
Viewed by 1285
Abstract
Soil microbial carbon use efficiency (CUE) is the core of the soil carbon (C) cycle that captures a dual microbial control point between soil organic C (SOC) accumulation and loss. The interpretation of these patterns and drivers of microbial CUE after long-term afforestation [...] Read more.
Soil microbial carbon use efficiency (CUE) is the core of the soil carbon (C) cycle that captures a dual microbial control point between soil organic C (SOC) accumulation and loss. The interpretation of these patterns and drivers of microbial CUE after long-term afforestation remains, however, a major scientific challenge. In particular, there are major uncertainties about the role of microbial traits in driving CUE. Here, we compared sites along a 45-year afforestation chronosequence and combined the novel 18O-H2O tracer method with metagenomic analysis to quantify CUE and explore the mechanisms underlying microbe-mediated C dynamics. The results showed that soil microbial CUE significantly increased following afforestation and showed a positive relationship with SOC, which suggested that microbial CUE could promote C accumulation in afforested ecosystems. We further found the critical role of microbial traits in the regulation of CUE through altering microbial life history strategies: microbial CUE was positively and significantly correlated with resource acquisition (A) genes, but showed a negative and significant correlation with stress tolerance (S) strategy genes. These results suggested that soil microbes reduce investment in S strategies and shift to A and high yield (Y) strategies, thereby increasing CUE. This knowledge is important because it advances our understanding of the microbial physiological and evolutionary tradeoffs mediating soil C cycling in the context of human-induced land use change. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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13 pages, 2908 KB  
Article
Soil Nitrogen Mineralization Is Driven by Functional Microbiomes Across a North–South Forest in China
by Hongyan Cheng, Minshu Yuan, Chengjie Ren, Fazhu Zhao and Jun Wang
Microorganisms 2025, 13(12), 2799; https://doi.org/10.3390/microorganisms13122799 - 9 Dec 2025
Viewed by 826
Abstract
Nitrogen (N) mineralization is a complex microbial-driven process that controls the supply of N for plants and microbes. The relative contribution of different microbial N-cycling species/genes to the variation in N mineralization rate (NMR) across contrasting forest biomes was unclear. Here, we investigate [...] Read more.
Nitrogen (N) mineralization is a complex microbial-driven process that controls the supply of N for plants and microbes. The relative contribution of different microbial N-cycling species/genes to the variation in N mineralization rate (NMR) across contrasting forest biomes was unclear. Here, we investigate the linkages between soil metagenomes and N mineralization rates across 10 contrasting forest biomes (covering temperate, subtropical, and tropical forests) along a 3425 km north–south forest in China. We found that the NMR was higher in subtropical forests, and the variation in NMR can be explained by climate and soil environments, particularly for soil substrate NH4+. Similar to NMR, microbial N-cycling genes/species were also higher in subtropical forests, suggesting that the higher microbial N-cycling traits in warm regions may drive higher NMR. We also quantified the contribution of microbial N-cycling gene pathways to NMR across forest biomes and found that the microbial N-denitrification pathway (genes like norZ, narG, nirK, and norB) and nitrification pathway (genes like nxr) explained more variation in NMR than other pathways, such as N ammonification. Collectively, our work demonstrates the importance of microbial N-cycling traits to explain soil N mineralization rates across forest biomes and suggests that this information can be used to help improve the management of the N cycle in forests across biomes. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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Review

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19 pages, 2799 KB  
Review
Research Progress on Rhizosphere Microbiota for Controlling Soil-Borne Diseases: Mechanisms, Applications, and Challenges
by Yong Liu, Xiaofang Sun, Jia Lai, Shugu Wei, Yuzhen Sheng, Yinchao Zhang, Qianfang Zhang, Pengsheng Ye, Ling Huang and Hualan Zeng
Microorganisms 2026, 14(4), 900; https://doi.org/10.3390/microorganisms14040900 - 16 Apr 2026
Cited by 1 | Viewed by 1382
Abstract
Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant’s ‘second genome’, plays a pivotal role [...] Read more.
Soil-borne diseases pose a severe threat to global agricultural production and food security. Traditional chemical control methods face significant challenges, including environmental pressure, pathogen resistance, and food safety concerns. The rhizosphere microbial community, often termed the plant’s ‘second genome’, plays a pivotal role in maintaining plant health and defending against pathogen invasion. Recent advances in multi-omics technologies, synthetic microbial communities (SynComs) construction, and rhizosphere metabolomics have significantly advanced our understanding of the mechanisms by which rhizosphere microbiomes suppress soil-borne diseases. This review systematically summarizes the following: 1. key drivers of rhizosphere microbial community assembly, particularly plant “cry for help” signaling; 2. core beneficial microbial taxa and their disease-suppressive mechanisms; 3. the critical role of microbial interaction networks; 4. microbiome-based management strategies and their application progress; and 5. current challenges and future research directions. Compared with previous reviews that separately discussed rhizosphere microbiota, disease-suppressive soils, synthetic microbial communities (SynComs), or prebiotics, this review uniquely integrates multiple levels of regulation, from plant genetic determinants (‘M genes’) and root exudate-mediated ‘crying for help’ to microbiome engineering (SynComs and prebiotics) and cross-kingdom interactions (bacteria–fungi–protists–phages). A central conceptual axis of ‘M genes → microbiome engineering → breeding’ is proposed, bridging plant genetics, microbial ecology, and crop improvement for durable disease suppression. Ultimately, this work aims to provide a theoretical foundation for developing efficient and sustainable green control technologies against soil-borne diseases. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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