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Microorganisms
Special Issues
Diversity, Function, and Ecology of Soil Microbial Communities, Second Edition
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Diversity, Function, and Ecology of Soil Microbial Communities, Second Edition

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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 1195

Editor

Prof. Dr. Adijailton José de Souza

E-Mail Website
Guest Editor
Program of Agricultural Microbiology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
Interests: agronomy; soil microbiology; pesticide environmental behavior; microbial ecology; composing; plant growth-promoting bacteria; biological control; sewage treatment and agricultural use; regenerative agriculture; biological nitrogen fixation; pesticide biod
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Diversity, Function and Ecology of Soil Microbial Communities” (https://www.mdpi.com/journal/microorganisms/special_issues/I5374588V0). 

Soil microbial communities are fundamental to ecosystem functioning, driving key processes such as nutrient cycling, organic matter decomposition, and plant health. Their diversity reflects a complex interplay of biotic and abiotic factors, including soil type, climate, vegetation, and land use. Recent advances in molecular and metagenomic techniques have revealed extraordinary taxonomic and functional diversity within these communities, uncovering new microbial taxa and metabolic pathways. This diversity supports critical ecological functions, from nitrogen fixation to carbon sequestration, and mediates soil resilience to environmental stressors. Understanding structure–function relationships in soil microbiomes is essential for predicting ecosystem responses to global climate change and for developing sustainable agricultural practices. This Special Issue highlights current research on the composition, functional roles, and ecological interactions of soil microorganisms, emphasizing their importance in maintaining soil health, as well as the stability and resilience of agroecosystems to ensure food security and sustainability. The scope of this Special Issue covers research on soil microbiomes; land use change and its impact on soil health; advances in biotechnology to promote soil and plant health; responses of the soil microbiome to inputs of synthetic microbial communities; and microbial ecology.

Prof. Dr. Adijailton José de Souza
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 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 microbial communities
  • metabolic pathways
  • ecological functions
  • agroecosystems

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Related Special Issue

Published Papers (2 papers)

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Research

16 pages, 7391 KB  
Article
Altitudinal Patterns of Diversity, Stability, and Niche Breadth in Faba Bean Rhizosphere Bacterial Communities on the Qinghai Plateau
by Huilin Yan, Panda Ye, Huigang Pei, Jiajia He and Yujiao Liu
Microorganisms 2026, 14(9), 1901; https://doi.org/10.3390/microorganisms14091901 - 27 Aug 2026
Viewed by 230
Abstract
This study characterized regional variation in faba bean rhizosphere bacterial communities across a broad survey of the Qinghai Plateau and examined their associations with soil and spatial factors. Rhizosphere soil samples were collected from 15 faba bean-growing field sites across Haidong City, Xining [...] Read more.
This study characterized regional variation in faba bean rhizosphere bacterial communities across a broad survey of the Qinghai Plateau and examined their associations with soil and spatial factors. Rhizosphere soil samples were collected from 15 faba bean-growing field sites across Haidong City, Xining City, and Hainan Tibetan Autonomous Prefecture, Qinghai Province, China, spanning elevations from 1842.9 to 3206.3 m. Nine within-site subsamples were collected at each field site, with the field site treated as the independent unit of replication. Soil physicochemical properties were measured, and bacterial communities were characterized by high-throughput sequencing of the 16S rRNA gene. At the site level, bacterial alpha-diversity indices showed numerical variation among the three regional elevation groups, but did not differ significantly. Bacterial community composition differed among groups in the site-level PERMANOVA based on Bray–Curtis dissimilarities (pseudo-F2.12 = 1.789, R2 = 0.230, p = 0.031), although substantial overlap among sites remained. However, a conservative locality-level sensitivity analysis was not significant (p = 0.060). Geographic distance was significantly associated with bacterial community dissimilarity, whereas elevation difference showed no detectable independent association after controlling for geographic distance, indicating a substantial contribution of spatial structure to the observed community differentiation. Dominant phylum-level composition was broadly conserved across sites, while genus-level relative abundances showed descriptive spatial variation. Neither RAVD-based compositional consistency nor community-level niche breadth differed significantly among groups. Among the measured soil properties, only pH differed significantly, whereas most nutrient variables did not. Overall, the study revealed spatially structured regional differentiation in faba bean rhizosphere bacterial communities across the Qinghai Plateau. The observed patterns likely reflect the combined influence of geographic structure, elevation, background soil conditions, agricultural management, plant phenology, and other unmeasured environmental factors, which could not be independently disentangled in the present survey. Full article
(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities, Second Edition)
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10 pages, 3480 KB  
Article
Diversity of Soil Fungi, Entomopathogenic Fungi and Their Driving Factors in the Eastern Tanggula Mountains in the Qinghai–Tibet Plateau
by Langba Danzeng, Gadan Langjie, Yao Xiao, Danzeng Luobu, Jinxing Li and Dun Wang
Microorganisms 2026, 14(7), 1507; https://doi.org/10.3390/microorganisms14071507 - 10 Jul 2026
Viewed by 501
Abstract
This study aims to elucidate the soil fungal community structure, the distribution of entomopathogenic fungi (EPF) resources, and their driving mechanisms in the alpine grassland of the northern side of the eastern Tanggula Mountains in the Qinghai–Tibet Plateau. Five representative sites were established [...] Read more.
This study aims to elucidate the soil fungal community structure, the distribution of entomopathogenic fungi (EPF) resources, and their driving mechanisms in the alpine grassland of the northern side of the eastern Tanggula Mountains in the Qinghai–Tibet Plateau. Five representative sites were established along an elevational gradient of 4000–5100 m, and 15 soil samples were collected. High-throughput sequencing (ITS region) and an insect baiting method were combined to analyze fungal community composition and diversity. LEfSe analysis, random forest modeling, redundancy analysis (RDA), and network analysis were employed to reveal the environmental driving mechanisms of community assembly. A total of 412 fungal species belonging to 303 genera were annotated, with Ascomycota as the dominant phylum. At the high-elevation site Jie-duo Town, Zaduo County (ZD-JD), the cold-tolerant ectomycorrhizal fungus Inocybe was absolutely dominant (17.18%). The low-elevation site Dong-ba Town, Nangqian County (NQ-DB), was enriched with the saprotrophic genus Mortierella (10.34%) and EPF taxa. The mid-elevation site Zhuo-xiao Town, Nangqian County (NQ-ZX), was characterized by Solicocozyma (11.88%) and exhibited the highest network complexity. Alpha diversity decreased with increasing elevation. A total of 35 EPF strains were isolated via the baiting method, predominantly Metarhizium anisopliae, M. brunneum, and M. robertsii, with the highest number of isolates (16 strains) recovered from NQ-DB. Elevation indirectly drove community assembly by regulating temperature and plant productivity. The soil fungal community structure in the alpine grassland of the eastern Tanggula Mountains exhibits significant spatial heterogeneity along the elevational gradient. Low-elevation habitats serve as hotspots for EPF resources, while high-elevation isolates harbor potential stress-resistance genes. The combination of culture-dependent and sequencing-based approaches provides a reliable strategy for microbial resource surveys in extreme environments. Full article
(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities, Second Edition)
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