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Microorganisms
Special Issues
Soil Microbiome and Ecological Biogeochemical Cycles
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Soil Microbiome and Ecological Biogeochemical Cycles

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 3585

Special Issue Editors

Dr. Giorgia Santini

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Guest Editor
Department of Biology, University of Naples Federico II, 80126 Naples, Italy
Interests: soil biodiversity; microorganisms; decomposers; n cycles; microbiome
Special Issues, Collections and Topics in MDPI journals
Dr. Lucia Santorufo

E-Mail Website
Guest Editor
Department of Biology, University of Naples Federico II, 80126 Naples, Italy
Interests: soil biodiversity; forest fires; soil fauna; microarthropods; nutrient cycle
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Soil microorganisms shape the cycles of life and death. To date, molecular biology techniques have brought us closer to discovering which microorganisms live in soil and play a key role in the soil ecosystem. All the microorganisms in the soil microbial community contribute to the health of the ecosystem, but there is limited scientific knowledge about the species that affect biogeochemical cycles and could be used as bioindicators. This Special Issue aims to explore the functional role of soil microorganisms in the biogeochemical cycles on which theoretical ecology is based.

Dr. Giorgia Santini
Dr. Lucia Santorufo
Guest Editors

Manuscript Submission Information

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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 ecology
  • soil ecosystem
  • microorganisms functional role
  • microorganisms functional group
  • key species
  • biogeochemical cycles
  • microbiome
  • soil community

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Published Papers (4 papers)

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Research

13 pages, 1253 KiB  
Article
Excessive Extracellular Ammonium Production by a Free-Living Nitrogen-Fixing Soil Clostridium sp. Strain
by Soyeon Park and Jeonghwan Jang
Microorganisms 2024, 12(12), 2634; https://doi.org/10.3390/microorganisms12122634 - 19 Dec 2024
Viewed by 539
Abstract
A Gram-positive, rod-shaped, and obligate anaerobic bacterial strain OS1-26 was isolated from apple orchard soil in Iksan, South Korea. Interestingly, strain OS1-26 was observed to possess the functional genes involved in biological nitrogen fixation (BNF), including nifH, which was actively transcribed during [...] Read more.
A Gram-positive, rod-shaped, and obligate anaerobic bacterial strain OS1-26 was isolated from apple orchard soil in Iksan, South Korea. Interestingly, strain OS1-26 was observed to possess the functional genes involved in biological nitrogen fixation (BNF), including nifH, which was actively transcribed during the anaerobic cultivation with excessive production of extracellular NH4+ despite of presence of other fixed N nutrients. The BNF of strain OS1-26 was distinguished from the other well-known Clostridium diazotrophs, such as C. pasteurianum and C. acetobutylicum. The altruistic N-fixing ability of the strain may play a pivotal role in providing N nutrients to the microbial community and plants in the soil ecosystem. The microorganism grew at 25–35 °C (optimum 30–35 °C) and pH 5.0–8.0 (optimum 6.0–8.0) but was not able to grow in the presence of >0.5% NaCl. The major cellular fatty acids of strain OS1-26 were C16:0, C14:0, and the summed feature consisted of C16:1 ω7c and C16:1 ω6c (35.63%, 25.29%, and 18.84%, respectively). The 16S rRNA phylogeny indicated that strain OS1-26 is a member of the genus Clostridium, and the closest species are C. aciditolerans, C. nitrophenolicum, and C. thailandense, with 16S rRNA sequence similarities such as 99.71%, 98.52%, and 98.45%, respectively. In spite of the high 16S rRNA sequence similarity, strain OS1-26 showed overall genomic relatedness, such as the average nucleotide identity (ANI), and phenotypical features distinctly different from Clostridium aciditolerans. Although the species taxonomy of strain OS1-26 is undetermined within the genus Clostridium based on overall genomic and phenotypic properties, further studies on the soil bacterial strain would enhance our understanding of its taxonomic identity, ecological roles for the terrestrial soil N cycle, and the potential to be developed as a biological N fertilizer. Full article
(This article belongs to the Special Issue Soil Microbiome and Ecological Biogeochemical Cycles)
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20 pages, 2934 KiB  
Article
Soil Microbial Communities Changes Along Depth and Contrasting Facing Slopes at the Parque Nacional La Campana, Chile
by Carolina Quinteros-Urquieta, Jean Pierre Francois, Polette Aguilar-Muñoz and Verónica Molina
Microorganisms 2024, 12(12), 2487; https://doi.org/10.3390/microorganisms12122487 - 3 Dec 2024
Viewed by 737
Abstract
The Parque Nacional La Campana (PNLC) was recently recognized for its high soil surface microbial richness. Here, we explored the microbial community structure in soil profiles from contrasting facing slopes where sclerophyllous forest (SF) and xerophytic shrubland (XS) develop. Soil physicochemical conditions (dry [...] Read more.
The Parque Nacional La Campana (PNLC) was recently recognized for its high soil surface microbial richness. Here, we explored the microbial community structure in soil profiles from contrasting facing slopes where sclerophyllous forest (SF) and xerophytic shrubland (XS) develop. Soil physicochemical conditions (dry density, pH, and organic matter C and N isotopic soil signatures) were determined at three depths (5, 10, and 15 cm depths). Amplicon sequencing (16S rRNA and ITS1-5F) and specific quantification (qPCR bacteria, archaea and ammonia-oxidizing archaea, fungi) were used to profile the microbial community. Our results indicate that opposite slopes, with different vegetation types and soil conditions studied potentially explained the spatial variability of the microbial community composition, especially between sites than through soil depth. Discriminative taxa were observed to vary between sites, such as, C. nitrososphaera (ammonia-oxidizing archaea) and Sphingomonas, and bacteria associated with Actinobacteria and Bacteroidetes were predominant in SF and XS, respectively. Fungi affiliated with Humicola and Preussia were more abundant in SF, while Cladosporium and Alternaria were in XS. Higher ASV richness was observed in SF compared to XS, for both prokaryotes and fungi. Furthermore, SF showed a higher number of shared ASVs, while XS showed a decrease in unique ASVs in deeper soil layers. In XS, the genus DA101 (Verrucomicrobia) increases with soil depth, reaching higher levels in SF, while Kaistobacter shows the opposite trend. PNLC soils were a reservoir of redundant microbial functions related to biogeochemical cycles, including symbiotic and phytopathogenic fungi. In conclusion, as with the predominant vegetation, the structure and potential function of microbial life in soil profiles were associated with the contrasting the effect of facing slopes as toposequence effects. Full article
(This article belongs to the Special Issue Soil Microbiome and Ecological Biogeochemical Cycles)
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14 pages, 2599 KiB  
Article
Fungal Footprints: Soil Fungal Communities in Black Walnut and Red Oak Forests
by Shaneka S. Lawson, Juan P. Frene and Niall D. Lue Sue
Microorganisms 2024, 12(11), 2184; https://doi.org/10.3390/microorganisms12112184 - 30 Oct 2024
Viewed by 816
Abstract
Soil fungal communities are critical for forest ecosystem functions in the Central Hardwood Region (CHR) of the USA. This evaluation, which took place in 2022–2023, investigates the influence of Juglans nigra (BW, black walnut) and Quercus rubra (NRO, Northern red oak) on soil [...] Read more.
Soil fungal communities are critical for forest ecosystem functions in the Central Hardwood Region (CHR) of the USA. This evaluation, which took place in 2022–2023, investigates the influence of Juglans nigra (BW, black walnut) and Quercus rubra (NRO, Northern red oak) on soil properties and fungal community structures across three CHR sites. The objectives of this study are to investigate how the fungal communities identified beneath J. nigra and Q. rubra serve to influence biodiversity and soil health within hardwood plantations. Soils from two locations in Indiana and one in Michigan were examined and assessed for variations in fungal composition and diversity. Soil fungal communities were characterized using Illumina high-throughput sequencing while multivariate analysis was applied to analyze patterns in these fungal communities. These data provided insights into how environment, location, and tree species affect fungal community structure. Results indicate that J. nigra soils exhibited higher carbon (0.36%, 1.02%, 0.72%), nitrogen (25%, 29%, 56%), and pH (0.46, 1.08, 1.54) levels than Q. rubra soils across all three sites and foster greater fungal diversity. Specifically, J. nigra was associated with increased Ascomycota diversity, whereas Q. rubra supported a higher prevalence of Basidiomycota. Basidiomycota were negatively correlated with carbon and pH, while Ascomycota showed positive correlations with these variables. These findings highlight how crucial it is to understand how different tree species influence fungal communities and, consequently, how they influence forest soil health. Our findings serve to improve forest management practices by emphasizing the importance of fungal communities in maintaining the function and resilience of an ecosystem. Our study underscores that grasping these specific interactions is essential for effective forest management, especially when considering how to use fungal communities to boost plant growth. This work focuses on hardwood plantations rather than either agricultural ecosystems, monocultures, or native forests, thus filling a gap in the current literature where many studies are limited to specific fungal groups such as mycorrhizae. In future research, it is important to examine a wider range of tree species. This will deepen our understanding of fungal community dynamics and their impact on maintaining healthy forest ecosystems. Our hardwood plantation focus also notes the potential for adaptive forest management as environmental conditions change. Full article
(This article belongs to the Special Issue Soil Microbiome and Ecological Biogeochemical Cycles)
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8 pages, 1317 KiB  
Communication
Intermediate Disturbances Enhance Microbial Enzyme Activities in Soil Ecosystems
by Hojeong Kang, Sunghyun Kim, Keunyea Song, Min-Jung Kwon and Jaehyun Lee
Microorganisms 2024, 12(7), 1401; https://doi.org/10.3390/microorganisms12071401 - 11 Jul 2024
Viewed by 1058
Abstract
The Intermediate Disturbance Hypothesis (IDH) posits that maximal plant biodiversity is attained in environments characterized by moderate ecological disturbances. Although the applicability of the IDH to microbial diversity has been explored in a limited number of studies, there is a notable absence of [...] Read more.
The Intermediate Disturbance Hypothesis (IDH) posits that maximal plant biodiversity is attained in environments characterized by moderate ecological disturbances. Although the applicability of the IDH to microbial diversity has been explored in a limited number of studies, there is a notable absence of experimental reports on whether soil microbial ‘activity’ demonstrates a similar response to the frequency or intensity of environmental disturbances. In this investigation, we conducted five distinct experiments employing soils or wetland sediments exposed to varying intensities or frequencies of disturbances, with a specific emphasis on disturbances associated with human activity, such as chemical contamination, hydrologic changes, and forest thinning. Specifically, we examined the effects of bactericide and heavy metal contamination, long-term drainage, tidal flow, and thinning management on microbial enzyme activities in soils. Our findings revealed that microbial enzyme activities were highest at intermediate disturbance levels. Despite the diversity in experiment conditions, each trial consistently demonstrated analogous patterns, suggesting the robustness of the IDH in elucidating microbial activities alongside diversity in soils. These outcomes bear significant implications for ecological restoration and management, as intermediate disturbance may expedite organic matter decomposition and nutrient cycles, crucial for sustaining ecosystem services in soils. Full article
(This article belongs to the Special Issue Soil Microbiome and Ecological Biogeochemical Cycles)
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