Microbiome Dynamics and Ecological Mechanisms Under Urbanization and Climate Change

A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: 31 January 2027 | Viewed by 1235

Special Issue Editors


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Guest Editor
Center for the Planetary Health and Innovation Science (PHIS), The IDEC Institute, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City 739-8511, Hiroshima, Japan
Interests: microbial genomics; metagenomics; microbial ecology; NTM; environmental infections
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Guest Editor Assistant
The IDEC Institute, Hiroshima University, Higashi-Hiroshima City 739-8511, Hiroshima, Japan
Interests: microbiomes; metagenomics; ecological forces; co-occurrence network; public health

Special Issue Information

Dear Colleagues,

Urbanization and global climate change are reshaping both natural and built environments, driving profound shifts in microbial ecosystems. As cities expand and environmental conditions become increasingly unpredictable, microbial communities in air, water, soil, and indoor environments are becoming increasingly exposed to anthropogenic stressors like pollution, urban heat islands, and biodiversity losses. These disruptions affect ecosystem functions and human health—through altered microbial networks, antimicrobial resistance, and links to allergic or infectious diseases. Understanding how urban development influences microbiomes is crucial for sustainable planning and One Health-based public health strategies.

Microbial communities form the unseen majority of Earth’s biodiversity and are critical to ecosystem functions like biogeochemical cycling and environmental resilience. Advances in sequencing, metagenomics, and ecological modeling have opened new avenues for exploring their diversity and functional traits under stress. Nevertheless, key questions remain regarding how microbes adapt to urban infrastructure, shifting climates, and human behavior. Addressing these requires cross-disciplinary and multi-scalar research approaches.

This Special Issue aims to bring together cutting-edge studies focusing on microbiome structure, ecological functions, and dynamic mechanisms under changing environments including nature and built environments. By highlighting microbial diversity, functional gene expression, and health-related implications, we aim to foster global collaboration and innovative solutions in urban microbial ecology and One Health.

Prof. Dr. Fumito Maruyama
Guest Editor

Dr. Yue Yin
Guest Editor Assistant

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Keywords

  • microbial diversity
  • microbiome function
  • climate change
  • urban ecosystems
  • ecophysiological mechanisms

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Published Papers (1 paper)

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Research

24 pages, 3752 KB  
Article
Fungal Diversity and Environmental Drivers in Soil and Litter Across a Pinus cembroides Forest Management Gradient in Its Southern Range Edge
by José Alfredo Jiménez-Rubio, Bernardo Águila, Rosario Medel-Ortiz, Bruno Chávez-Vergara, Jesús Pérez-Moreno and Roberto Garibay-Orijel
Diversity 2026, 18(5), 269; https://doi.org/10.3390/d18050269 - 30 Apr 2026
Viewed by 749
Abstract
Pinus cembroides is among the pine species best adapted to arid and semi-arid ecosystems in the Americas, and its potential distribution is projected to expand under climate change. However, the success of this expansion will depend on belowground processes, particularly the role of [...] Read more.
Pinus cembroides is among the pine species best adapted to arid and semi-arid ecosystems in the Americas, and its potential distribution is projected to expand under climate change. However, the success of this expansion will depend on belowground processes, particularly the role of soil fungal communities, which in subtropical forests are key for nutrient cycling and plant resilience to environmental stress. Yet their vertical stratification and responses to forest management remain poorly understood, especially in semi-arid systems. Here, we characterized fungal communities from mineral soil and litter associated with P. cembroides across a forest management gradient (mature forests, disturbed stands, and pine plantations) at the southern limit of the species’ distribution. We evaluated the influence of climatic, edaphic, vegetation structure, and microbial activity variables (soil moisture, precipitation, pH, tree density, vegetation cover, temperature and extracellular enzyme activity) on fungal community composition. We found strong vertical stratification between litter and mineral soil. When both substrates were analyzed together as an integrated soil profile, forest condition had no significant effect on alpha diversity; however, substrate-specific analyses revealed higher richness in mineral soil of mature forests compared to disturbed and plantation sites, while litter communities showed no significant differences among conditions. Litter communities were characterized by saprotrophic and endophytic fungi, whereas mineral soil communities were enriched in ectomycorrhizal and other root-associated taxa. Distance-based redundancy analysis indicated that fungal community composition was primarily associated with moisture content, precipitation, pH, tree density, and carbon-degrading enzyme activity. These results highlight the importance of substrate differentiation and environmental gradients in shaping fungal communities in semi-arid pine forests, and provide a baseline for understanding how management and climate change influence soil fungal diversity and ecosystem functioning. Full article
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