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

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 372

Special Issue Editor

Prof. Dr. Adijailton José de Souza

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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,

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, stability and resilience of agroecosystems to ensure food security and sustainability. The scope of this Special Issue covers research on soil microbiome, land use change and its impact on soil health; advances in biotechnology to promote soil and plant health; responses of the soil microbiome to input 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 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 microbial communities
  • metabolic pathways
  • ecological functions
  • agroecosystems

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Published Papers (2 papers)

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Research

18 pages, 2194 KB  
Article
Driving Effects of Soil Microbial Diversity on Soil Multifunctionality in Carya illinoinensis Agroforestry Systems
by Cheng Huang, Mengyu Zhou, Fasih Ullah Haider, Lin Wu, Jia Xiong, Songling Fu, Zhaocheng Wang, Fan Yang and Xu Li
Microorganisms 2025, 13(11), 2425; https://doi.org/10.3390/microorganisms13112425 - 23 Oct 2025
Abstract
Sustainable soil management requires striking a balance between productivity and soil health. While agroforestry practices are known to improve soil health and ecosystem functions, the contribution of microbial diversity to maintaining multifunctional soil processes in pecan (Carya illinoinensis) cultivation has yet [...] Read more.
Sustainable soil management requires striking a balance between productivity and soil health. While agroforestry practices are known to improve soil health and ecosystem functions, the contribution of microbial diversity to maintaining multifunctional soil processes in pecan (Carya illinoinensis) cultivation has yet to be fully elucidated. This study examined microbial diversity, soil functions, and multifunctionality across different pecan intercropping setups. We compared a monoculture pecan plantation with three agroforestry models: pecan–Paeonia suffruticosa–Hemerocallis citrina (CPH), pecan–P. suffruticosa (CPS), and pecan–P. lactiflora (CPL). We employed high-throughput sequencing (16S and ITS) to determine the soil bacterial and fungal communities and analyzed the species diversity, extracellular enzyme activities, and physicochemical properties. Soil multifunctionality (SMF) was evaluated using 20 indicators for nutrient supply, storage, cycling, and environmental regulation. Agroforestry increased soil fungal diversity and improved multifunctionality when compared to monoculture. The CPS and CPH models were the most beneficial, increasing multifunctionality by 0.74 and 0.55 units, respectively. Structural equation modeling revealed two key pathways: bacterial diversity significantly enhanced nutrient cycling and environmental regulation, whereas fungal diversity primarily promoted nutrient cycling. These pathways together delivered clear gains in multifunctionality. Random forest analysis identified key predictors (total nitrogen, total carbon, available potassium, β-1,4-N-acetylglucosaminidase, and alkaline phosphatase), highlighting the joint importance of nutrients and microbial enzymes. Our results demonstrate that selecting species in pecan agroforestry alters microbial communities and activates key functions that support soil health and long-term resilience. Hence, pecan agroforestry maintains SMF through microbial processes, with CPS showing the strongest effect. These results can inform species selection and encourage broader testing for resilient, biodiversity-based farming practices. Full article
(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)
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19 pages, 2329 KB  
Article
Linking Soil Microbial Diversity to Nitrogen and Phosphorus Dynamics
by Bruna Arruda, Eduardo Mariano, Wilfrand Ferney Bejarano-Herrera, Fábio Prataviera, Elizabeth Mie Hashimoto, Fernando Ferrari Putti, Jéssica Pigatto de Queiroz Barcelos, Paulo Sergio Pavinato, Fernando Dini Andreote and Davey L. Jones
Microorganisms 2025, 13(10), 2401; https://doi.org/10.3390/microorganisms13102401 - 21 Oct 2025
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Abstract
Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and [...] Read more.
Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and phosphorus (P) dynamics. The purposes of this study were as follows: (i) to characterize microbial activity after soil autoclaving through microbial 14CO2-respiration; and (ii) to evaluate the effect of microbial manipulation and autoclaving on soil N and 33P dynamics. For this, two sets of soil samples from two areas (forest and cultivated area) were used in the laboratory. Firstly, 14C-glucose was added to the soils and after 24 h five soil microbiomes were generated: AS (autoclaved soil), and AS re-inoculated with serial dilutions (w/v) prepared by successive mixing of soil suspensions in sterile deionized water obtaining 10−1, 10−3, and 10−6, which generated the treatments AS + 10−1, AS + 10−3, and AS + 10−6; and the treatment NS (non-autoclaved control), all incubated for 28 d. 14CO2 emission was used to characterize microbial activity; additionally, N dynamics were assessed at the end of incubation. In a second assay, 33P was applied to the soil before autoclaving and re-inoculation. Following further incubation (14 d), a 33P chemical fractionation was performed. The following are based on the results: (i) 14CO2 emission: microbial activity in the autoclaved soil is null, but after a reinoculation of AS + 10−1 and AS + 10−3 soil dilution suspension, the 14CO2-respiration is higher than in an NS. (ii) regarding the N dynamics, in autoclaved soils, the microbial levels increased N-NH4+ concentration, with an evident increase in the AS + 10−3 and AS + 10−1, and a reduction in the N-NO3− concentration in comparison to the NS. For 33P, the autoclaving procedure itself reduced the 33P lability, regardless of the levels of microbial community reinoculated. Full article
(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)
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