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Soil Systems
Special Issues
Microbial Community Structure and Function in Soils
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Microbial Community Structure and Function in Soils

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

Deadline for manuscript submissions: 30 January 2026 | Viewed by 4726

Special Issue Editors

Dr. Roberta Pastorelli

E-Mail Website
Guest Editor
Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), 50125 Florence, Italy
Interests: microbial ecology; microbial process in biogeochemical cycles; plant-associated bacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Sara Del Duca

E-Mail Website
Guest Editor
Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), 50125 Florence, Italy
Interests: environmental microbiology; soil health indicators; microbial communities
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Soil Systems aims to expand the current state of the art regarding soil microbial communities. Soils harbour the most diverse and complex microbiome on Earth. Soil microorganisms display high metabolic and functional diversity, being involved in nutrient and carbon transformations and shaping the soil habitat through various biogeochemical and biophysical mechanisms, thus representing a key factor of soil resilience. These functions are part of the basis of the so-called “ecosystem services”, which are vital to humans and the environment (e.g., provision of food, clean water, fibers, wood, carbon storage, regulation of climate and nutrient cycling). Microorganisms are therefore vital for the overall functioning, stability, and sustainability of the ecosystem, determining soil’s fertility and health.

Authors are invited to submit their works on soil microorganisms, including the characterization of their communities and their inter- and intra-kingdom interactions, the definition of their ecosystem functions, as well as the application of novel methodologies for the study of these communities. Research, review and opinion articles concerning our current knowledge of soil microbial communities and their ecosystem functions are invited.

Yours faithfully,

Dr. Roberta Pastorelli
Dr. Sara Del Duca
Guest Editors

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. Soil Systems is an international peer-reviewed open access quarterly 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 1800 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

  • edaphic communities
  • soil microorganisms
  • bacteria
  • fungi
  • archaea
  • protists
  • ecosystem services
  • ecosystem functions
  • nutrient cycling
  • soil health

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Published Papers (3 papers)

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Research

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17 pages, 4870 KiB  
Article
Microbial Diversity and Heavy Metal Resistome in Slag-Contaminated Soils from an Abandoned Smelter in Chihuahua, Mexico
by Gustavo Montes-Montes, Zilia Y. Muñoz-Ramírez, Leonor Cortes-Palacios, Javier Carrillo-Campos, Obed Ramírez-Sánchez, Ismael Ortiz-Aguirre, Laila N. Muñoz-Castellanos and Román González-Escobedo
Soil Syst. 2025, 9(2), 30; https://doi.org/10.3390/soilsystems9020030 - 1 Apr 2025
Viewed by 498
Abstract
Heavy metal(loid) (HM) contamination in soils from smelting activities poses significant environmental and public health risks, as well as disruptions in microbial community dynamics and HM resistance gene profiles. This study investigates the microbial diversity, resistome, and physicochemical properties of soils from the [...] Read more.
Heavy metal(loid) (HM) contamination in soils from smelting activities poses significant environmental and public health risks, as well as disruptions in microbial community dynamics and HM resistance gene profiles. This study investigates the microbial diversity, resistome, and physicochemical properties of soils from the abandoned Avalos smelter in Chihuahua, Mexico. Through soil analyses, we identified elevated concentrations of certain HMs, which pose serious environmental and health hazards. The metagenomic analysis of the microbial community, composed of bacteria, archaea, and fungi, was dominated by genera such as Streptomyces, Bradyrhizobium, Halobaculum, Nitrosocosmicus, Fusarium, and Aspergillus in rhizospheric soil. Furthermore, a diverse array of metal resistance genes (MRGs) were detected, associated with copper, arsenic, iron, lead, cadmium, zinc, and other HMs. Additionally, metagenome-assembled genomes (MAGs) revealed the presence of functional genes linked to HM resistance, providing deeper insights into the ecological roles and metabolic capabilities of microbial taxa. These findings highlight the significant impact of smelting-derived contamination on microbial diversity and functional potential, offering valuable insights for the development of bioremediation strategies in HM-contaminated environments. Full article
(This article belongs to the Special Issue Microbial Community Structure and Function in Soils)
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15 pages, 1906 KiB  
Article
Bacterial Communities Nodulating Lupinus cosentinii Gus. and Their Inputs in the Worldwide Phylogeography of Lupine Endosymbionts
by Mokhtar Rejili, Mohamed Ali Benabderrahim and Mohamed Mars
Soil Syst. 2024, 8(4), 119; https://doi.org/10.3390/soilsystems8040119 - 17 Nov 2024
Viewed by 1073
Abstract
Genetic variability in bacterial populations that nodulate Lupinus cosentinii in Tunisia was investigated. Phylogenetic studies of 40 isolates using recA partial sequences categorized them into three clusters within the Bradyrhizobium genus. Twenty-three strains selected from the three clusters were thoroughly examined through housekeeping [...] Read more.
Genetic variability in bacterial populations that nodulate Lupinus cosentinii in Tunisia was investigated. Phylogenetic studies of 40 isolates using recA partial sequences categorized them into three clusters within the Bradyrhizobium genus. Twenty-three strains selected from the three clusters were thoroughly examined through housekeeping genes (recA, glnII and rpoB) multilocus sequence analysis (MLSA). Our results showed that 23 representative strains were distributed in five distinct clusters, with 13 strains belonging to Bradyrhizobium canariense BTA-1T/Bradyrhizobium lupini USDA3051T (10 strains) and Bradyrhizobium hipponense aSej3T (three strains) lineages. Interestingly, eight strains occupied a separate position and could belong to two putative novel Bradyrhizobium species. The nodC phylogeny placed the 23 strains within three symbiovars: genistearum (19 strains), lupini (two strains) and, for the first time, the symbiovar cyanophyllae (two strains). Based on the worldwide phylogeography of rhizobial symbionts nodulating lupine (14 species), our results reported that eight species occurred in more than one continent, and six species were specific for one continent, e.g., Bradyrhizobium rifense, Bradyrhizobium diazoefficiens, Phyllobacterium sp. and Devosia sp. were specific to the African continent, the Bradyrhizobium iriomotense/Bradyrhizobium stylosanthis group to America, and Bradyrhizobium valentinum to the European continent. Full article
(This article belongs to the Special Issue Microbial Community Structure and Function in Soils)
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Review

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29 pages, 2253 KiB  
Review
Impact of Abiotic Stressors on Soil Microbial Communities: A Focus on Antibiotics and Their Interactions with Emerging Pollutants
by Abdul Rashid P. Rasheela, Muhammad Fasih Khalid, Dana A. Abumaali, Juha M. Alatalo and Talaat Ahmed
Soil Syst. 2025, 9(1), 2; https://doi.org/10.3390/soilsystems9010002 - 26 Dec 2024
Cited by 3 | Viewed by 1986
Abstract
Soil is a complex and dynamic ecosystem containing a diverse array of microorganisms, and plays a crucial and multifaceted role in various functions of the ecosystem. Substantial fluctuations in the environmental conditions arise from diverse global changes. The microbial shifts in the soil [...] Read more.
Soil is a complex and dynamic ecosystem containing a diverse array of microorganisms, and plays a crucial and multifaceted role in various functions of the ecosystem. Substantial fluctuations in the environmental conditions arise from diverse global changes. The microbial shifts in the soil in concordance with the changing environmental factors, or a combination of these factors, are of high significance. Exploring the contribution of global change drivers to the microbial community to improve the predictions of the response of the microbial community to the functioning of the ecosystem is of prime importance. Promoting the health of soil microorganisms maintains the overall health and fertility of the soil, which in turn supports the health of terrestrial ecosystems and agricultural systems. The current review aims to assemble different abiotic factors or stressors that exist in the environment that affect the microbial community. More focus will be given to one of the stressors—antibiotics, a recent emerging pollutant. The effects on the soil microbial community and the future of soil health due to the presence of antibiotics will be addressed. The scope of the interaction of antibiotics with other pollutants like plastics and heavy metals (HMs) will be examined. Full article
(This article belongs to the Special Issue Microbial Community Structure and Function in Soils)
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