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Microorganisms
Special Issues
Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes
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Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 2233

Special Issue Editor

Dr. Xiawei Peng

E-Mail Website
Guest Editor
College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
Interests: bioremediation and safety assessment of polluted environment; waste biological treatment and resource utilization technology; microbial molecular ecology

Special Issue Information

Dear Colleagues,

Soil microbial communities serve as fundamental regulators of terrestrial ecosystem processes, mediating biogeochemical cycles through complex interactions with plants across multiple spatial scales. Recent advances have revealed how these intricate plant–microbe–soil networks govern ecosystem functioning through sophisticated metabolic coupling and signaling cascades. However, critical knowledge gaps persist, limit our understanding of (1) the scaling relationships between microbial community dynamics and ecosystem processes; (2) the evolutionary ecology of plant–microbiome symbioses; (3) the context dependency of these interactions across different ecosystems; and (4) the emergent properties arising from plant–soil–microbiome feedback.

This Special Issue will explore the latest advances in soil microbiome research, from molecular mechanisms to ecological applications. We welcome studies on microbial diversity, plant–microbe interactions, functional genomics, and the role of microbes in soil health in different landscapes and under the effects of global climatic change. Contributions may address fundamental ecology, novel methodologies, or applied solutions for sustainable ecosystems and environmental management.

Dr. Xiawei Peng
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. 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 assembly
  • microbial functional traits
  • ecological networks
  • metagenomics
  • plant–soil feedback
  • climate change adaptation
  • microbiome engineering
  • ecosystem services
  • sustainable land management
  • soil biodiversity conservation

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Published Papers (3 papers)

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Research

21 pages, 3781 KB  
Article
Environmental Effects on Bacterial Community Assembly in Arid and Semi-Arid Grasslands
by Shenggang Chen, Yaqi Zhang, Jun Ma, Mingyue Bai, Yinglong Chen, Jianbin Guo and Lin Chen
Microorganisms 2025, 13(8), 1934; https://doi.org/10.3390/microorganisms13081934 - 19 Aug 2025
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Abstract
Studying the effects of environmental factors on microbial community assemblies is crucial for understanding microbial biodiversity and ecosystem processes. Although numerous studies have explored the spatial patterns of microbial communities in surface soils, bacterial community distributions in subsurface layers remain poorly understood. We [...] Read more.
Studying the effects of environmental factors on microbial community assemblies is crucial for understanding microbial biodiversity and ecosystem processes. Although numerous studies have explored the spatial patterns of microbial communities in surface soils, bacterial community distributions in subsurface layers remain poorly understood. We investigated multiple community metrics of soil bacteria in arid and semi-arid grasslands in China, and the V4 region of 16S rDNA was analyzed using soil property measurements, fluorescent PCR, and high-throughput sequencing techniques. Specifically, copiotrophic taxa dominate the topsoil, whereas oligotrophic taxa are prevalent in nutrient-limited subsoil. Bacterial diversity decreases from the topsoil to subsoil, and bacterial distribution and ecological community composition exhibit a strong dependence on environmental factors. Moreover, microbial interaction networks demonstrated a progressive simplification with increasing soil depth: topsoil communities displayed higher modularity and a greater prevalence of positive interactions, whereas subsoil networks were significantly less complex. Null model analyses evidenced assembly mechanisms: deterministic processes (particularly homogeneous selection) dominated the bacterial community assembly, but their influence weakened with depth, whereas stochastic processes (e.g., dispersal limitation) increased progressively from the topsoil to subsoil. The PLS-PM analysis demonstrated that the relative influence of abiotic factors (e.g., climatic conditions and nutrient availability), biotic factors (interspecific interactions), along with drift and dispersal limitations on fungal community assembly exhibited depth-dependent patterns. This study provides novel insights into the vertical stratification of bacterial community in arid and semi-arid grasslands, and advances our understanding of pedogenic process under climate change and microbial adaptive strategies in heterogeneous soil environments. Full article
(This article belongs to the Special Issue Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes)
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24 pages, 3691 KB  
Article
Independent and Interactive Effects of Precipitation Intensity and Duration on Soil Microbial Communities in Forest and Grassland Ecosystems of China: A Meta-Analysis
by Bo Hu and Wei Li
Microorganisms 2025, 13(8), 1915; https://doi.org/10.3390/microorganisms13081915 - 17 Aug 2025
Viewed by 479
Abstract
Altered precipitation regimes, both in intensity and duration, can profoundly influence the structure and function of soil microbial communities, yet the patterns and drivers of these responses remain unclear across ecosystem types. Here, using data exclusively from 101 field experiments conducted in China [...] Read more.
Altered precipitation regimes, both in intensity and duration, can profoundly influence the structure and function of soil microbial communities, yet the patterns and drivers of these responses remain unclear across ecosystem types. Here, using data exclusively from 101 field experiments conducted in China (yielding 695 observations), we investigated the impacts of altered precipitation on soil microbial biomass, diversity, and enzymatic activity in forest and grassland ecosystems. Soil microbial biomass carbon (MBC) and nitrogen (MBN) increased in response to precipitation addition, particularly in grasslands, but they decreased under reduced precipitation, with the decline being more pronounced in forests. The magnitude and duration of precipitation manipulation significantly influenced these effects, with moderate and long-term changes producing divergent responses. Bacterial diversity was largely unaffected by all precipitation treatments, whereas fungal diversity decreased significantly under intense and short-term reductions in precipitation. Enzyme activities exhibited the following element-specific patterns: carbon- and phosphorus-cycling enzymes and antioxidant enzymes were suppressed by precipitation reduction, especially in grasslands, while nitrogen-cycling enzymes showed no consistent response. Moreover, microbial responses were significantly shaped by environmental factors, including mean annual temperature (MAT), mean annual precipitation (MAP), and elevation. Our region-specific analysis highlights precipitation-driven microbial dynamics across China’s diverse climatic and ecological conditions. These findings demonstrate that soil microbial communities respond asymmetrically to precipitation changes, with responses shaped by both ecosystem type and climatic context, underscoring the need to account for environmental heterogeneity when predicting belowground feedback to climate change. Full article
(This article belongs to the Special Issue Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes)
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19 pages, 2862 KB  
Article
Characterization of Soil Bacterial Communities in Different Vegetation Types on the Lava Plateau of Jingpo Lake
by Yanli Zhang, Jiaxing Huang, Jiaxin Xue, Kaining Zhang, Xintong Chen, Jianhui Jia and Qingyang Huang
Microorganisms 2025, 13(7), 1648; https://doi.org/10.3390/microorganisms13071648 - 11 Jul 2025
Viewed by 484
Abstract
To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical [...] Read more.
To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical properties were identified among these types (p < 0.05). The soil bacterial community structures also varied significantly (p < 0.05), with Actinobacteriota, Proteobacteria, and Acidobacteria as the dominant phyla, exhibiting notable genus-level differences (p < 0.05). The soil organic matter (SOM), available nitrogen (AN), total nitrogen (TN), and soil water content (SWC) were significantly correlated with the bacterial community structure (p < 0.05 or p < 0.01), acting as key determinants of the microbial community structure and function. PICRUSt2 functional predictions revealed significant variations in the metabolic functions of the soil bacterial communities across vegetation types, indicating distinct functional specializations. In conclusion, the Jingpo Lake lava plateau harbors abundant bacterial resources. When devising vegetation adaptation strategies, it is essential to take into account variations in the rhizosphere soil bacteria across different vegetation types. Furthermore, prioritizing the implementation of forest vegetation is crucial in the adaptive management of the lava plateau. This approach holds significant implications for studying the bacterial diversity in the lava plateau and exploring the cultivation and application of functional bacteria in extreme environments. Full article
(This article belongs to the Special Issue Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes)
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