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Microorganisms
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Advances in Soil Microbial Ecology
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Advances in Soil Microbial Ecology

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

Deadline for manuscript submissions: 15 June 2024 | Viewed by 4084

Special Issue Editors

Dr. Jie Wang

E-Mail Website
Guest Editor
Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, China
Interests: plant-soil-microbe interaction; soil microbiology; restoration ecology; land use change; soil carbon; vegetation restoration; soil conversation; global change; soil phosphorus
Dr. Yadong Xu

E-Mail Website
Guest Editor
School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
Interests: soil nitrogen cycle; soil microecology; stoichiometric ratio; community diversity; community assembly processes

Special Issue Information

Dear Colleagues,

Soil, a complex and dynamic ecosystem, harbors an incredibly diverse and intricate community of microorganisms that play fundamental roles in nutrient cycling, organic matter decomposition, plant health, and overall ecosystem functioning. The study of soil microbial ecology offers insights into the interactions between microorganisms, plants, and their environment, shedding light on the intricate web of life beneath our feet. This Special Issue aims to delve into the multifaceted realm of soil microbial ecology, exploring the interactions, functions, and adaptations of soil microorganisms that collectively shape terrestrial ecosystems.

The Special Issue invites the submission of original research articles, reviews, and perspectives that span a wide spectrum of topics within soil microbial ecology, including, but not limited to:

  • Microbial diversity and community structure in different soil types and ecosystems;
  • Microbial interactions and their roles in nutrient cycling and organic matter decomposition;
  • Impact of soil microorganisms on plant health, growth, and nutrient acquisition;
  • Responses of soil microbial communities to environmental changes and disturbances;
  • Microbial contributions to soil carbon and nitrogen dynamics;
  • Role of soil microorganisms in ecosystem resilience and restoration;
  • Advances in molecular techniques for studying soil microbial communities;
  • Microbial contributions to soil ecosystem services and sustainable agriculture.

Dr. Jie Wang
Dr. Yadong Xu
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. 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 microorganisms
  • microbial ecology
  • microbial community
  • microbial diversity
  • microbial interactions
  • soil ecosystem
  • nutrient cycle

Published Papers (5 papers)

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Research

20 pages, 4848 KiB  
Article
Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics
by Rui Li, Haihua Jiao, Bo Sun, Manjiao Song, Gaojun Yan, Zhihui Bai, Jiancheng Wang, Xuliang Zhuang and Qing Hu
Microorganisms 2024, 12(4), 683; https://doi.org/10.3390/microorganisms12040683 - 28 Mar 2024
Viewed by 590
Abstract
Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the [...] Read more.
Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity’s critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology)
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12 pages, 5463 KiB  
Article
Comparison of Microbial Diversity of Two Typical Volcanic Soils in Wudalianchi, China
by Qingyang Huang, Fan Yang, Hongjie Cao, Jiahui Cheng, Mingyue Jiang, Maihe Li, Hongwei Ni and Lihong Xie
Microorganisms 2024, 12(4), 656; https://doi.org/10.3390/microorganisms12040656 - 26 Mar 2024
Viewed by 554
Abstract
Volcanic lava is an excellent model of primary succession, in which basalt-associated microorganisms drive the cycling of different elements such as nitrogen, carbon, and other nutrients. Microbial communities in volcanic soils are of particular interest for study on the emergence and evolution of [...] Read more.
Volcanic lava is an excellent model of primary succession, in which basalt-associated microorganisms drive the cycling of different elements such as nitrogen, carbon, and other nutrients. Microbial communities in volcanic soils are of particular interest for study on the emergence and evolution of life within special and extreme conditions. The initial processes of colonization and subsequent rock weathering by microbial communities are still poorly understood. We analyzed the soil bacterial and fungal communities and diversities associated with lava (LBL) and kipuka (BK) sites in Wudalianchi using 16S and ITS rRNA Illumina Miseq sequencing techniques. The results showed that soil physical and chemical properties (pH, MC, TOC, TN, TP, AP, DOC, and DON) significantly differed between LBL and BK. The Shannon, Ace, and Pd indexes of fungi in the two sites showed a significant difference (p < 0.05). The dominant bacterial phyla forming communities at LBL and BK sites were Acidobacteria, Proteobacteria, Actinobacteria, and Basidiomycota, and their differences were driven by Gemmatimonadetes and Verrucomicrobia. The dominant fungal phyla of LBL and BK sites were Ascomycota, Zygomycota, and Rozellomcota, which differed significantly between the two sites. The microbial communities showed extremely significant differences (p < 0.05), with MC, pH, and nitrogen being the main influencing factors according to RDA/CCA and correlation analysis. Microbial functional prediction analysis across the two sites showed that the relative abundance of advantageous functional groups was significantly different (p < 0.05). The combined results drive us to conclude that the volcanic soil differences in the deposits appear to be the main factor shaping the microbial communities in Wudalianchi (WDLC) volcanic ecosystems. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology)
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17 pages, 4616 KiB  
Article
Nitrogen Application and Rhizosphere Effect Exert Opposite Effects on Key Straw-Decomposing Microorganisms in Straw-Amended Soil
by Yuanzheng Zhao, Shiyu Wang, Meiling Zhang, Li Zeng, Liyu Zhang, Shuyu Huang, Rong Zhang, Wei Zhou and Chao Ai
Microorganisms 2024, 12(3), 574; https://doi.org/10.3390/microorganisms12030574 - 13 Mar 2024
Viewed by 650
Abstract
Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season [...] Read more.
Crop residue decomposition is an important part of the carbon cycle in agricultural ecosystems, and microorganisms are widely recognized as key drivers during this process. However, we still know little about how nitrogen (N) input and rhizosphere effects from the next planting season impact key straw-decomposing microbial communities. Here, we combined amplicon sequencing and DNA-Stable Isotope Probing (DNA-SIP) to explore these effects through a time-series wheat pot experiment with four treatments: 13C-labeled maize straw addition with or without N application (S1N1 and S1N0), and no straw addition with or without N application (S0N1 and S0N0). The results showed that straw addition significantly reduced soil microbial alpha diversity in the early stages. Straw addition changed microbial beta diversity and increased absolute abundance in all stages. Growing plants in straw-amended soil further reduced bacterial alpha diversity, weakened straw-induced changes in beta diversity, and reduced bacterial and fungal absolute abundance in later stages. In contrast, N application could only increase the absolute abundance of soil bacteria and fungi while having little effect on alpha and beta diversity. The SIP-based taxonomic analysis of key straw-decomposing bacteria further indicated that the dominant phyla were Actinobacteria and Proteobacteria, with overrepresented genera belonging to Vicinamibacteraceae and Streptomyces. Key straw-decomposing fungi were dominated by Ascomycota, with overrepresented genera belonging to Penicillium and Aspergillus. N application significantly increased the absolute abundance of key straw-decomposing microorganisms; however, this increase was reduced by the rhizosphere effect. Overall, our study identified key straw-decomposing microorganisms in straw-amended soil and demonstrated that they exhibited opposite responses to N application and the rhizosphere effect. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology)
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31 pages, 10999 KiB  
Article
The Molecular Profile of Soil Microbial Communities Inhabiting a Cambrian Host Rock
by Ting Huang, Daniel Carrizo, Laura Sánchez-García, Qitao Hu, Angélica Anglés, David Gómez-Ortiz, Liang-Liang Yu and David C. Fernández-Remolar
Microorganisms 2024, 12(3), 513; https://doi.org/10.3390/microorganisms12030513 - 02 Mar 2024
Viewed by 963
Abstract
The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering [...] Read more.
The process of soil genesis unfolds as pioneering microbial communities colonize mineral substrates, enriching them with biomolecules released from bedrock. The resultant intricate surface units emerge from a complex interplay among microbiota and plant communities. Under these conditions, host rocks undergo initial weathering through microbial activity, rendering them far from pristine and challenging the quest for biomarkers in ancient sedimentary rocks. In addressing this challenge, a comprehensive analysis utilizing Gas Chromatography Mass Spectrometry (GC-MS) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) was conducted on a 520-Ma-old Cambrian rock. This investigation revealed a diverse molecular assemblage with comprising alkanols, sterols, fatty acids, glycerolipids, wax esters, and nitrogen-bearing compounds. Notably, elevated levels of bacterial C16, C18 and C14 fatty acids, iso and anteiso methyl-branched fatty acids, as well as fungal sterols, long-chained fatty acids, and alcohols, consistently align with a consortium of bacteria and fungi accessing complex organic matter within a soil-type ecosystem. The prominence of bacterial and fungal lipids alongside maturity indicators denotes derivation from heterotrophic activity rather than ancient preservation or marine sources. Moreover, the identification of long-chain (>C22) n-alkanols, even-carbon-numbered long chain (>C20) fatty acids, and campesterol, as well as stigmastanol, provides confirmation of plant residue inputs. Furthermore, findings highlight the ability of contemporary soil microbiota to inhabit rocky substrates actively, requiring strict contamination controls when evaluating ancient molecular biosignatures or extraterrestrial materials collected. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology)
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15 pages, 31140 KiB  
Article
The Characteristics of the Root-Zone Soil’s Biological Properties and Microbial Community Structure in Grafted Star Anise Plantations
by Jian Xiao, Junxian Liu, Siyu Wu, Wenhui Liang and Shangdong Yang
Microorganisms 2024, 12(3), 431; https://doi.org/10.3390/microorganisms12030431 - 20 Feb 2024
Viewed by 700
Abstract
Extensive management seriously affects the output, quality, and sustainable development of star anise, and grafting is commonly used to improve its production and quality. Although many studies have explored the effects of grafting on soil microorganisms for other plants, there is a lack [...] Read more.
Extensive management seriously affects the output, quality, and sustainable development of star anise, and grafting is commonly used to improve its production and quality. Although many studies have explored the effects of grafting on soil microorganisms for other plants, there is a lack of research on aromatic plants, especially on the soil ecosystems of star anise plantations. The effect of grafting star anise on the soil’s biological characteristics and microbial composition remains unclear. The soil’s enzyme activities, soil microbial biomass, and microbial community composition in grafted and non-grafted star anise plantations in Guangxi, China were studied using high-throughput sequencing technology. The results showed that the microbial biomass carbon and phosphorus contents in the soils of grafted star anise were significantly lower and the phosphatase activity was significantly higher than in the soils of non-grafted star anise. In comparison with the soils of non-grafted star anise plantations, the proportions of Proteobacteria, Acidobacteria, Actinobacteria, and WPS-2 decreased and the proportions of Chloroflexi, Planctomycetes, and Verrucomicrobia increased in the grafted star anise plantations. Meanwhile, Bacteroidetes was a dominant bacterial phylum unique to the soil of the grafted star anise plantations. Moreover, the proportions of Ascomycota and Basidiomycota increased and the proportions of Mortierellomycota and unclassified_k_Fungi decreased in the soils of the grafted star anise plantations. Furthermore, Basidiomycota and Rozellomycota had significant dominance in the grafted star anise plantations. In general, grafting can improve soil fertility and maintain soil health by promoting soil nutrient cycling and increasing the soil’s microbial diversity. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology)
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