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

Deadline for manuscript submissions: 15 April 2025 | Viewed by 6825

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Dr. Dan Xiao

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Guest Editor

Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
Interests: nutrient cycling; vegetation recovery; microbial biodiversity; soil carbon; soil nitrogen
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Yinhang Xia

E-Mail Website
Guest Editor Assistant

Department of Agricultural Resources and Environment, Hunan Agricultural University, Changsha 410128, China
Interests: soil organic carbon; soil organic nitrogen cycling; microbial metabolic processes; agricultural ecosystems

Special Issue Information

Dear Colleagues,

Soil nutrient cycles involving microorganisms play a crucial role in enhancing soil fertility, promoting plant growth, controlling pathogens and pests, improving soil structure, and maintaining ecosystem functions. These processes are affected by environmental changes, such as global climate warming, nitrogen deposition, heavy metal pollution, waste disposal, and agricultural management practices. The role of soil microorganisms in organic matter turnover, nitrogen cycling, phosphorus transformations, and metal sequestration in natural and agricultural ecosystems is crucial for sustainable ecosystem management. This Special Issue aims to explore the functions of soil microorganisms in nutrient cycling and how they enhance the multifunctionality of ecosystems, providing fundamental and practical guidance for sustainable soil management. The potential topics include the following:

Microbial involvement in soil nutrient cycling.
The diversity, community structure, and characteristics of key functional soil microorganisms and microbial food webs.
Applications of soil microorganisms in vegetation restoration and agricultural production.
The effects of global warming, nitrogen deposition, and agricultural management practices on soil microbial communities.
Soil microorganisms in environmental remediation and soil erosion control. This Special Issue is open to fundamental, applied, and field research and review manuscripts on all aspects of these topics.

Dr. Dan Xiao
Guest Editor

Prof. Dr. Yinhang Xia
Guest Editor Assistant

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 microbiome
nutrient cycling
soil micro-food web
land-use change
ecosystem restoration
agricultural management

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Published Papers (8 papers)

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Research

16 pages, 10589 KiB

Open AccessArticle

Effects of Increasing the Nitrogen–Phosphorus Ratio on the Structure and Function of the Soil Microbial Community in the Yellow River Delta

by Jinzhao Ma, Zehao Zhang, Jingkuan Sun, Tian Li, Zhanyong Fu, Rui Hu and Yao Zhang

Microorganisms 2024, 12(12), 2419; https://doi.org/10.3390/microorganisms12122419 - 25 Nov 2024

Viewed by 279

Abstract

Nitrogen (N) deposition from human activities leads to an imbalance in the N and phosphorus (P) ratios of natural ecosystems, which has a series of negative impacts on ecosystems. In this study, we used 16s rRNA sequencing technology to investigate the effect of the N-P supply ratio on the bulk soil (BS) and rhizosphere soil (RS) bacterial community of halophytes in coastal wetlands through manipulated field experiments. The response of soil bacterial communities to changing N and P ratios was influenced by plants. The N:P ratio increased the α-diversity of the RS bacterial community and changed the structure of the BS bacterial community. P addition may increase the threshold, causing decreased α-diversity of the bacterial community. The co-occurrence network of the RS community is more complex, but it is more fragile than that of BS. The co-occurrence network in BS has more modules and fewer network hubs. The increased N:P ratio can increase chemoheterotrophy and denitrification processes in the RS bacterial community, while the N:P ratio can decrease the N-fixing processes and increase the nitration processes. The response of the BS and the RS bacterial community to the N:P ratio differed, as influenced by soil organic carbon (SOC) content in terms of diversity, community composition, mutualistic networks, and functional composition. This study demonstrates that the effect of the N:P ratio on soil bacterial community is different for plant roots and emphasizes the role of plant roots in shaping soil bacterial community during environmental change. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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16 pages, 2615 KiB

Open AccessArticle

Metagenomic Analysis Reveals the Effects of Different Land Use Types on Functional Soil Phosphorus Cycling: A Case Study of the Yellow River Alluvial Plain

by Ming Wen, Yu Liu, Chaoyang Feng and Zhuoqing Li

Microorganisms 2024, 12(11), 2194; https://doi.org/10.3390/microorganisms12112194 - 30 Oct 2024

Viewed by 541

Abstract

Phosphorus (P) is a crucial limiting nutrient in soil ecosystems, significantly influencing soil fertility and plant productivity. Soil microorganisms adapt to phosphorus deficiency and enhance soil phosphorus effectiveness through various mechanisms, which are notably influenced by land use practices. This study examined the impact of different land use types (long-term continuous maize farmland, abandoned evolving grassland, artificial tamarisk forests, artificial ash forests, and wetlands) on soil phosphorus-cycling functional genes within the Tanyang Forest Farm in a typical region of the Yellow River alluvial plain using macro genome sequencing technology. The gene cluster related to inorganic phosphorus solubilization and organic phosphorus mineralization exhibited the highest relative abundance across different land use types (2.24 × 10⁻³), followed by the gene cluster associated with phosphorus transport and uptake (1.42 × 10⁻³), with the lowest relative abundance observed for the P-starvation response regulation gene cluster (5.52 × 10⁻⁴). Significant differences were found in the physical and chemical properties of the soils and the relative abundance of phosphorus-cycling functional genes among various land use types. The lowest relative abundance of soil phosphorus-cycling functional genes was observed in forestland, with both forestland types showing significantly lower gene abundance compared to wetland, farmland, and grassland. Correlation analysis and redundancy analysis (RDA) revealed a significant relationship between soil physicochemical properties and soil phosphorus-cycling functional genes, with ammonium nitrogen, organic carbon, total nitrogen, and pH being the main environmental factors influencing the abundance of these genes, explaining 70% of the variation in their relative abundance. Our study reveals land use’s impact on soil phosphorus-cycling genes, offering genetic insights into microbial responses to land use changes. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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15 pages, 4303 KiB

Open AccessArticle

Soil Properties Regulate Soil Microbial Communities During Forest Succession in a Karst Region of Southwest China

by Shanghua Jiang, Min Song, Hu Du, Feng Wang, Tongqing Song, Huijun Chen, Fuping Zeng and Wanxia Peng

Microorganisms 2024, 12(11), 2136; https://doi.org/10.3390/microorganisms12112136 - 24 Oct 2024

Viewed by 437

Abstract

Natural vegetation restoration has emerged as an effective and rapid approach for ecological restoration in fragile areas. However, the response of soil microorganisms to natural succession remains unclear. To address this, we utilized high-throughput sequencing methods to assess the dynamics of soil bacterial and fungal communities during forest succession (shrubland, secondary forest, and primary forest) in a karst region of Southwest China. Our study revealed that bacterial α-diversity was significantly higher in secondary forest compared to both shrubland and primary forest. Intriguingly, the soil bacterial community in primary forest exhibited a closer resemblance to that in shrubland yet diverged from the community in secondary forest. Conversely, the soil fungal community underwent notable variations across the different forest stages. Furthermore, analysis of the microbial co-occurrence network revealed that, within these karst forests, the relationships among soil fungi were characterized by fewer but stronger interactions compared to those among bacteria. Additionally, soil properties (including pH, soil organic carbon, total nitrogen, moisture, and available potassium), soil microbial biomass (specifically phosphorus and nitrogen), and plant diversity were the drivers of soil bacterial community dynamics. Notably, soil pH accounted for the majority of the variations observed in the soil fungal community during karst forest succession. Our findings provide valuable insights that can inform the formulation of strategies for ecological restoration and biodiversity conservation in karst regions, particularly from a microbial perspective. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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15 pages, 9123 KiB

Open AccessArticle

The Process of Soil Carbon Sequestration in Different Ecological Zones of Qingtu Lake in the Arid–Semi-Arid Region of Western China

by Tao Wang, Shengyin Zhang, Shuncun Zhang, Ming Shao, Zhaoyun Ding, Yanfang Zhou and Cuicui Su

Microorganisms 2024, 12(11), 2122; https://doi.org/10.3390/microorganisms12112122 - 23 Oct 2024

Viewed by 455

Abstract

As a vital component of the global carbon pool, soils in arid and semi-arid regions play a significant role in carbon sequestration. In the context of global warming, increasing temperatures and moisture levels promote the transformation of barren land into wetlands, enhancing carbon sinks. However, the overdevelopment of oases and excessive extraction of groundwater lead to the opposite effect, reducing carbon sequestration. This study examines two soil types—meadow soil (MS) and swamp soil (SS)—from Qingtu Lake, an arid lake in western China. It analyzes the sources of soil inorganic carbon, the composition and origin of dissolved organic matter (DOM), and the relationships between microbes, soil organic carbon (SOC), soil inorganic carbon (SIC), mineral composition, and soil texture. The results indicate that inorganic carbon in the study area consists of both primary carbonate minerals and secondary pedogenic carbonates. The DOM primarily consists of two components, both identified as terrestrial humic substances. In meadow soils, bacterial activity drives the weathering of plagioclase, which releases Ca²⁺ necessary for the formation of pedogenic carbonates. Plagioclase also provides colonization sites for microbes and, along with microbial activity, participates in the soil carbon cycle. Within the soil community, bacteria appear to play a more critical role than fungi. In contrast, microbial contributions to the carbon cycle in swamp soils are weaker, with minerals predominantly interacting with organic carbon to form mineral-associated organic matter, thus promoting the soil carbon cycle. These findings have important implications for understanding soil carbon sinks under different micro-ecological conditions in arid and semi-arid regions. Through targeted human intervention, it is possible to enhance carbon sequestration in these areas, contributing to the mitigation of global climate change. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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20 pages, 4889 KiB

Open AccessArticle

Effects of Wildfire on Soil CO₂ Emission and Bacterial Community in Plantations

by Yu Yang, Xuehui Liu, Shilin Huang, Jinchen Jia, Chuangye Wang, Lening Hu, Ke Li and Hua Deng

Microorganisms 2024, 12(8), 1666; https://doi.org/10.3390/microorganisms12081666 - 13 Aug 2024

Viewed by 978

Abstract

In order to study the effects of wildfires on soil carbon dioxide (CO₂) emissions and microbial communities in planted forests, Pinus massoniana Lamb. and Cunninghamia lanceolata (Lamb.) Hook. forests were selected as the research subjects. Through a culture test with 60 days of indoor constant temperature, the soil physical and chemical properties, organic carbon mineralization, organic carbon components, enzyme activity, and microbial community structure changes of the two plantations after fire were analyzed. The results showed that wildfires significantly reduced soil CO₂ emissions from the Pinus massoniana forests and Cunninghamia lanceolata forests by 270.67 mg·kg⁻¹ and 470.40 mg·kg⁻¹, respectively, with Cunninghamia lanceolata forests exhibiting the greatest reduction in soil CO₂ emissions compared to unburned soils. Bioinformatics analysis revealed that the abundance of soil Proteobacteria in the Pinus massoniana and Cunninghamia lanceolata forests decreased by 6.00% and 4.55%, respectively, after wildfires. Additionally, redundancy analysis indicated a significant positive correlation between Proteobacteria and soil CO₂ emissions, suggesting that the decrease in Proteobacteria may inhibit soil CO₂ emissions. The Cunninghamia lanceolata forests exhibited a significant increase in soil available nutrients and inhibition of enzyme activities after the wildfire. Additionally, soil CO₂ emissions decreased more, indicating a stronger adaptive capacity to environmental changes following the wildfire. In summary, wildfire in the Cunninghamia lanceolata forests led to the most pronounced reduction in soil CO₂ emissions, thereby mitigating soil carbon emissions in the region. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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20 pages, 8912 KiB

Open AccessArticle

Short-Term Effects of Cenchrus fungigraminus/Potato or Broad Bean Interplanting on Rhizosphere Soil Fertility, Microbial Diversity, and Greenhouse Gas Sequestration in Southeast China

by Jing Li, Yufang Lei, Yeyan Wen, Jieyi Zhu, Xiaoyue Di, Yi Zeng, Xiao Han, Zuhui Que, Hatungimana Mediatrice, Christopher Rensing, Zhanxi Lin and Dongmei Lin

Microorganisms 2024, 12(8), 1665; https://doi.org/10.3390/microorganisms12081665 - 13 Aug 2024

Viewed by 1016

Abstract

Cenchrus fungigraminus is a new species and is largely used as forage and mushroom substrate. However, it can usually not be planted on farmland on account of local agricultural land policy. Interplanting Cenchrus fungigraminus with other crops annually (short-term) is an innovative strategy to promote the sustainable development of the grass industry in southern China. To further investigate this, C. fungigraminus mono-planting (MC), C. fungigraminus–potato interplanting (CIP) and C. fungigraminus–broad bean interplanting (CIB) were performed. Compared to MC, soil microbial biomass carbon (SMBC), soil organic matter (SOM), ammoniacal nitrogen (AMN), pH and soil amino sugars had a positive effect on the rhizosphere soil of CIP and CIB, as well as enhancing soil nitrogenase, nitrite reductase, and peroxidase activities (p < 0.05). Moreover, CIP improved the root vitality (2.08 times) and crude protein (1.11 times). In addition, CIB enhanced the crude fiber of C. fungigraminus seedlings. These two interplanting models also improved the microbial composition and diversity (Actinobacteria, Firmicutes, and Bacteroidota, etc.) in the rhizosphere soil of C. fungigraminus seedlings. Among all the samples, 189 and 59 genes were involved in methane cycling and nitrogen cycling, respectively, which improved the presence of the serine cycle, ribulose monophosphate, assimilatory nitrate reduction, methane absorption, and glutamate synthesis and inhibited denitrification. Through correlation analysis and the Mantel test, the putative functional genes, encoding functions in both nitrogen and methane cycling, were shown to have a significant positive effect on pH, moisture, AMN, SOM, SMBC, and soil peroxidase activity, while not displaying a significant effect on soil nitrogenase activity and total amino sugar (p < 0.05). The short-term influence of the interplanting model was shown to improve land use efficiency and economic profitability per unit land area, and the models could provide sustainable agricultural production for rural revitalization. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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16 pages, 4493 KiB

Open AccessArticle

Synthetic Microbial Community Promotes Bacterial Communities Leading to Soil Multifunctionality in Desertified Land

by Xinwei Hao, Yazhou Gu, Hongzhi Zhang, Xiao Wang, Xiaozhen Liu, Chunlei Chen, Congcong Wang, Xiaoqing Zhang, Xingyu Liu and Xihui Shen

Microorganisms 2024, 12(6), 1117; https://doi.org/10.3390/microorganisms12061117 - 30 May 2024

Cited by 2 | Viewed by 1128

Abstract

Soil desertification is an important challenge in global soil management, and effectively and stably restoring soil function is an urgent problem. Using synthetic microbial communities (SynComs) is a burgeoning microbial strategy aimed at enhancing soil nutrients through functional synergies among diverse microorganisms; nevertheless, their effectiveness in restoring desertified soils remains unknown. In this study, we conducted a two-year field experiment using a SynCom constructed by in situ probiotic bacteria and set up control, chemical fertilizer, and combined SynCom–chemical fertilizer (combined fertilizer) treatments to investigate the linkage between microbial communities and soil multifunctionality in the soil surface layer (0–10 cm). Both the bacterial and fungal communities differed the most under the combined fertilizer treatment compared to the control. The bacterial communities differed more under treatments of the SynCom than the chemical fertilizer, while the fungal communities differed more under the chemical fertilizer treatment than the SynCom treatment. Regarding soil function, the SynCom strengthened the correlation between enzyme activities and both bacterial communities and functional properties. pH and available potassium were the main influencing factors under the chemical fertilizer and combined fertilizer treatments. The beta-diversity of the bacterial communities was significantly correlated with soil multifunctionality. Random forest analyses showed that the SynCom significantly enhanced the bacterial communities, driving soil multifunctionality, and that some potential microbial taxa drove multiple nutrient cycles simultaneously. In summary, the SynCom effectively increased the abundance of most carbon, nitrogen, and phosphorus functional genes as well as soil enzyme activities. The bacterial community composition contributed significantly to soil multifunctionality. Hence, the development of novel microbial agents holds significant potential for improving soil functionality and managing desertification. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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15 pages, 2944 KiB

Open AccessArticle

Bacteria, Fungi, and Protists Exhibit Distinct Responses to Managed Vegetation Restoration in the Karst Region

by Can Xiao, Dan Xiao, Mingming Sun and Kelin Wang

Microorganisms 2024, 12(6), 1074; https://doi.org/10.3390/microorganisms12061074 - 26 May 2024

Viewed by 992

Abstract

Bacteria, fungi, and protists occupy a pivotal position in maintaining soil ecology. Despite limited knowledge on their responses to managed vegetation restoration strategies in karst regions, we aimed to study the essential microbial communities involved in the process of vegetation restoration. We compared microbial characteristics in four land use types: planted forests (PF), forage grass (FG), a mixture of plantation forest and forage grass (FF), and cropland (CR) as a reference. Our findings revealed that the richness of bacteria and protists was higher in FF compared to PF, while fungal richness was lower in both PF and FF than in CR. Additionally, the bacterial Shannon index in FF was higher than that in CR and PF, while the fungal and protist Shannon indices were similar across all four land use types. Significant differences were observed in the compositions of bacterial, fungal, and protist communities between FF and the other three land use types, whereas bacterial, fungal, and protist communities were relatively similar in PF and FG. In FF, the relative abundance of bacterial taxa Acidobacteria, Firmicutes, and Gemmatimonadetes was significantly higher than in PF and CR. Fungal communities were dominated by Ascomycota and Basidiomycota, with the relative abundance of Ascomycota significantly higher in FF compared to other land use types. Regarding protistan taxa, the relative abundance of Chlorophyta was higher in FF compared to CR, PF, and FG, while the relative abundance of Apicomplexa was higher in CR compared to FF. Importantly, ammonium nitrogen, total phosphorus, and microbial biomass nitrogen were identified as key soil properties predicting changes in the diversity of bacteria, fungi, and protists. Our results suggest that the microbial community under FF exhibits greater sensitivity to vegetation restoration compared to PF and FG. This sensitivity may stem from differences in soil properties, the formation of biological crusts and root systems, and management activities, resulting in variations in bacterial, fungal, and protist diversity and taxa in PF. As a result, employing a combination restoration strategy involving plantation forest and forage grass proves to be an effective approach to enhance the microbial community and thereby improve ecosystem functionality in ecologically fragile areas. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling)

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