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Microorganisms
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Advances in Soil Microbial Ecology, 2nd Edition
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Advances in Soil Microbial Ecology, 2nd Edition

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 5022

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
Special Issues, Collections and Topics in MDPI journals
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 Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Advances in Soil Microbial Ecology”.

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

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Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (4 papers)

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Research

20 pages, 1870 KiB  
Article
Irrigation System, Rather than Nitrogen Fertilizer Application, Affects the Quantities of Functional Genes Related to N2O Production in Potato Cropping
by Laura Charlotte Storch, Katharina Schulz, Jana Marie Kraft, Annette Prochnow, Liliane Ruess, Benjamin Trost and Susanne Theuerl
Microorganisms 2025, 13(4), 741; https://doi.org/10.3390/microorganisms13040741 - 25 Mar 2025
Cited by 1 | Viewed by 200
Abstract
The spatial and temporal distribution of water and nitrogen supply affects soil-borne nitrous oxide (N2O) emissions. In this study, the effects of different irrigation technologies (no irrigation, sprinkler irrigation and drip irrigation) and nitrogen (N) application types (no fertilizer, broadcasted and [...] Read more.
The spatial and temporal distribution of water and nitrogen supply affects soil-borne nitrous oxide (N2O) emissions. In this study, the effects of different irrigation technologies (no irrigation, sprinkler irrigation and drip irrigation) and nitrogen (N) application types (no fertilizer, broadcasted and within irrigation water) on N2O flux rates and the quantities of functional genes involved in the N cycle in potato cropping were investigated over an entire season. The volume of irrigation water affected microbial N2O production, with the highest N2O flux rates found under sprinkler irrigation conditions, followed by drip and no irrigation. Nitrifier denitrification was identified as the potential pre-dominant pathway stimulated by fluctuations in aerobic-anaerobic soil conditions, especially under sprinkler irrigation. Regarding the different N application types, increased N use efficiency under fertigation was expected. However, N2O flux rates were not significantly reduced compared to broadcasted N application under drip irrigation. On average, the N2O fluxes were higher during the first half of the season, which was accompanied by a low N use efficiency of the potato crops. Potato crops mainly require N at later growth stages. Due to the different water and nutrient demand of potatoes, an adjusted application of fertilizer and water based on crop demand could reduce N2O emissions. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)
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17 pages, 3197 KiB  
Article
Responses of Soil Microbial Communities Associated with Phosphorus Transformation to Land-Use Alternations in a Meadow Grassland, Northeast China
by Li Yu, Ying Zhang, Zhenbo Cui and Chengyou Cao
Microorganisms 2025, 13(3), 624; https://doi.org/10.3390/microorganisms13030624 - 8 Mar 2025
Viewed by 736
Abstract
Land-use changes in meadow grasslands in semi-arid areas usually significantly affect soil environment and microbiota. However, studies on the response of soil P-cycle-related microbial communities to land-use conversions are still limited. In this study, a series of land-use types including upland field, paddy [...] Read more.
Land-use changes in meadow grasslands in semi-arid areas usually significantly affect soil environment and microbiota. However, studies on the response of soil P-cycle-related microbial communities to land-use conversions are still limited. In this study, a series of land-use types including upland field, paddy field, poplar plantation, and their adjacent natural meadow grassland in the Horqin Sandy Land of Northeast China were selected, and the diversities and structures of soil microbial communities involved in organic P mineralization (phoD-harboring community) and inorganic phosphate solubilization (gcd-harboring community) were investigated by the high-throughput sequencing technique. Land-use type had significant influences on soil physicochemical properties, enzymatic activities, and P conversion rates, thereby altering the structures of soil gcd and phoD communities. Soil phoD microbes are more abundant and have more contributions to available P than gcd microbes. The responses of gcd or phoD communities to land-use type were characterized as the quantitative shift in the relative abundance of dominant taxa; however, the basic compositions of the two communities were slightly affected. Soil pH, EC, and nutrient contents (including organic matter and total and available N, P, and K) all significantly affected soil gcd and phoD microbial communities. The abundance of phoD and gcd genes varied with land-use type and could be used as indicators for estimating the bioavailability of soil P. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)
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19 pages, 3427 KiB  
Article
Microbial Composition Change and Heavy Metal Accumulation in Response to Organic Fertilization Reduction in Greenhouse Soil
by Qin Qin, Jun Wang, Lijuan Sun, Shiyan Yang, Yafei Sun and Yong Xue
Microorganisms 2025, 13(1), 203; https://doi.org/10.3390/microorganisms13010203 - 18 Jan 2025
Cited by 1 | Viewed by 970
Abstract
Increased application of organic fertilizer is an effective measure to improve greenhouse soil quality. However, prolonged and intensive application of organic manure has caused nutrient and certain heavy metal accumulation in greenhouse soil. Therefore, the optimal quantity of organic manure required to sustain [...] Read more.
Increased application of organic fertilizer is an effective measure to improve greenhouse soil quality. However, prolonged and intensive application of organic manure has caused nutrient and certain heavy metal accumulation in greenhouse soil. Therefore, the optimal quantity of organic manure required to sustain soil fertility while mitigating the accumulation of heavy metals and other nutrients resulting from continuous application remains unclear. This study evaluated the impacts of sustained and reduced organic manure application on soil physicochemical properties, heavy metal contents, and microbial community through a 9-year greenhouse field experiment. Treatments included a control without any fertilizer (CK), conventional manure (M), and three reduced manure treatments (−25%M, −37.5%MNPK, and −50%MNPK). Compared to CK, either M treatment or manure reduction treatments either maintained or significantly elevated soil pH and soil organic matter, total nitrogen, total phosphorus, and available phosphorus. Notably, −37.5%MNPK exhibited further increases in the available nitrogen and potassium. The M treatment significantly increased in the total concentrations of cadmium, copper, lead, zinc, and the availability of chromium and zinc. However, reduced manure treatments showed no change or a significantly reduced in heavy metal availability. The −25%M and −37.5%MNPK treatments significantly improved bacterial diversity. Reducing organic manure altered microbial taxa abundance. The soil pH emerged as the primary driving factor for variation in the bacterial community structure, whereas available nitrogen, potassium, and lead were the key factors influencing fungal community structural changes. These results indicate that reducing excessive organic manure input is an effective strategy to control heavy metal accumulation, enhance soil fertility, and optimize microbial community structure. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)
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17 pages, 8788 KiB  
Article
Effects of Deep Tillage on Rhizosphere Soil and Microorganisms During Wheat Cultivation
by Junkang Sui, Chenyu Wang, Feifan Hou, Xueting Shang, Qiqi Zhao, Yuxuan Zhang, Yongqiang Hou, Xuewen Hua and Pengfei Chu
Microorganisms 2024, 12(11), 2339; https://doi.org/10.3390/microorganisms12112339 - 16 Nov 2024
Cited by 1 | Viewed by 1356
Abstract
The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. [...] Read more.
The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. Accordingly, we aimed to clarify the influence of DT on rhizosphere soil (RS) microbial communities and its possible contribution to the improvement of soil quality. Soil fertility was evaluated by analyzing several soil characteristics. High-throughput sequencing techniques were utilized to explore the structure and function of rhizosphere microbial communities. Despite lowered fertility levels in the 0–20 cm DT soil layer, significant variations were noted in the microbial composition of the DT wheat rhizosphere, with Acidobacteria and Proteobacteria being the most prominent. Furthermore, the abundance of Bradyrhizobacteria, a nitrogen-fixing bacteria within the Proteobacteria phylum, was significantly increased. A significant increase in glycoside hydrolases within the DT group was observed, in addition to higher abundances of amino acid and carbohydrate metabolism genes in the COG and KEGG databases. Moreover, DT can enhance soil quality and boost crop productivity by modulating soil microorganisms’ carbon and nitrogen fixation capacities. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)
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