Soil Microbial Ecology and Ecosystem Sustainability in a Changing Environment

A special issue of Soil Systems (ISSN 2571-8789).

Deadline for manuscript submissions: 28 February 2026 | Viewed by 515

Special Issue Editor


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Guest Editor
CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
Interests: soil viral ecology; soil carbon cycling; plant-microbe interactions; rhizosphere microbial community assembly; prophage

Special Issue Information

Dear Colleagues,

Soil microorganisms are critical components of the micro-food web and play pivotal roles in driving essential soil ecosystem functions. They significantly influence soil fertility, plant productivity, and overall ecosystem sustainability. Advancing research in soil microbial ecology is fundamental for improving our understanding of ecosystem processes and services, especially in the context of global environmental changes. This Special Issue will emphasize recent advancements in deciphering the complexity of soil microbial communities, focusing on their structure, functionality, and interactions with both biotic and abiotic factors. A thorough understanding of microbial-mediated soil processes, particularly those involved in nutrient cycling, soil fertility, and ecosystem resilience, will be highlighted.

Key areas of interest will include microbial biogeography and diversity patterns across ecosystems, along with the identification of the drivers shaping microbial community assembly. Such insights are crucial for understanding the ecological significance of microbial diversity in soil ecosystems. Additionally, investigations into soil micro-food webs—where the interactions among microbes, protists, nematodes, and other microfauna govern biodiversity and soil health—will be explored in detail. Emerging research on soil viral ecology will also be included, with a focus on how viruses regulate microbial dynamics and influence biogeochemical cycles in soil environments. Studies on microbial contributions to biogeochemical cycling need to emphasize feedback mechanisms linked to soil ecosystem services and climate change. The ecological impacts of antibiotic resistance genes (ARGs) in soil ecosystems, addressing their spread, horizontal gene transfer, and microbial adaptation, will be a prominent topic. The influence of emerging pollutants, such as microplastics and nanomaterials, on soil microbial communities will also be covered, alongside microbial resilience and remediation strategies. The rhizosphere microbiome and its role in plant growth promotion, stress tolerance, and plant–microbe–soil feedback mechanisms will receive significant attention. Interdisciplinary submissions that not only deepen our fundamental knowledge of soil microbial ecology but also propose practical applications for agriculture, environmental management, and climate change mitigation are encouraged. This Special Issue aims to become a cornerstone reference for researchers, policymakers, and practitioners interested in the multifaceted roles of soil microbiomes in sustaining ecosystem services.

Dr. Xiaolong Liang
Guest Editor

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Keywords

  • microbial biogeography
  • nutrient cycling
  • micro-food web
  • soil fertility
  • rhizosphere microbiome
  • bioremediation
  • soil viral ecology
  • climate change and soil health

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Published Papers (2 papers)

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Research

18 pages, 1595 KiB  
Article
An Analysis of Soil Nematode Communities Across Diverse Horticultural Cropping Systems
by Ewa M. Furmanczyk, Dawid Kozacki, Morgane Ourry, Samuel Bickel, Expedito Olimi, Sylvie Masquelier, Sara Turci, Anne Bohr, Heinrich Maisel, Lorenzo D’Avino and Eligio Malusà
Soil Syst. 2025, 9(3), 77; https://doi.org/10.3390/soilsystems9030077 (registering DOI) - 14 Jul 2025
Viewed by 51
Abstract
The analysis of soil nematode communities provides information on their impact on soil quality and the health of different agricultural cropping systems and soil management practices, which is necessary to evaluate their sustainability. Here, we evaluated the status of nematode communities and trophic [...] Read more.
The analysis of soil nematode communities provides information on their impact on soil quality and the health of different agricultural cropping systems and soil management practices, which is necessary to evaluate their sustainability. Here, we evaluated the status of nematode communities and trophic groups’ abundance in fifteen fields hosting different cropping systems and managed according to organic or conventional practices. The nematode population densities differed significantly across cropping systems and management types covering various European climatic zones (spanning 121 to 799 individuals per sample). Population density was affected by the duration of the cropping system, with the lowest value in the vegetable cropping system (on average about 300 individuals) and the highest in the long-term fruiting system (on average more than 500 individuals). The occurrence and abundance of the different trophic groups was partly dependent on the cropping system or the management method, particularly for the bacteria, fungal and plant feeders. The taxonomical classification of a subset of samples allowed us to identify 22 genera and one family (Dorylaimidae) within the five trophic groups. Few taxa were observed in all fields and samples (i.e., Rhabditis and Cephalobus), while Aphelenchoides or Pratylenchus were present in the majority of samples. Phosphorus content was the only soil chemical parameter showing a positive correlation with total nematode population and bacterial feeders’ absolute abundance. Based on the nematological ecological indices, all three cropping systems were characterized by disturbed soil conditions, conductive and dominated by bacterivorous nematodes. This knowledge could lead to a choice of soil management practices that sustain a transition toward healthy soils. Full article
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19 pages, 2419 KiB  
Article
Microbial Community Shifts and Functional Constraints of Dechlorinators in a Legacy Pharmaceutical-Contaminated Soil
by Xinhong Gan, Qian Liu, Xiaolong Liang, Yudong Chen, Yang Xu and Tingting Mu
Soil Syst. 2025, 9(3), 65; https://doi.org/10.3390/soilsystems9030065 - 25 Jun 2025
Viewed by 248
Abstract
Soil microbial communities are essential for the natural attenuation of organic pollutants, yet their ecological responses under long-term contamination remain insufficiently understood. This study examined the bacterial community structure and the abundance of dechlorinating bacteria at a decommissioned pharmaceutical-chemical site in northern Jiangsu [...] Read more.
Soil microbial communities are essential for the natural attenuation of organic pollutants, yet their ecological responses under long-term contamination remain insufficiently understood. This study examined the bacterial community structure and the abundance of dechlorinating bacteria at a decommissioned pharmaceutical-chemical site in northern Jiangsu Province, China, where the primary pollutants were dichloromethane, 1,2-dichloroethane, and toluene. Eighteen soil samples from the surface (0.2 m) and deep (2.2 m) layers were collected using a Geoprobe-7822DT system and analyzed for physicochemical properties and microbial composition via 16S rRNA gene amplicon sequencing. The results showed that the bacterial community composition was significantly shaped by the soil pH, moisture content, pollutant type, and depth. Dechlorinating bacteria were detected at all sites but exhibited low relative abundance, with higher concentrations in the surface soils. Desulfuromonas, Desulfitobacterium, and Desulfovibrio were the dominant dechlorinators, while Dehalococcoides appeared only in the deep soils. A network analysis revealed positive correlations between the dechlorinators and BTEX-degrading and fermentative taxa, indicating potential cooperative interactions in pollutant degradation. However, the low abundance of dechlorinators suggests that the intrinsic bioremediation capacity is limited. These findings provide new insights into microbial ecology under complex organic pollution, and support the need for integrated remediation strategies that enhance microbial functional potential in legacy-contaminated soils. Full article
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