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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: closed (31 July 2025) | Viewed by 3216

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Special Issue Editors

Dr. Qin Qin

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Guest Editor

Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Interests: soil remediation; soil remediation technology; solute transport; solute transformation; soil improvement; soil fertility enhancement; contaminated soil; microbial remediation

Dr. Jun Wang

E-Mail Website
Guest Editor

1. Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
2. Key Laboratory of Low-Carbon Green Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai 201403, China
3. Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Interests: soil microbial ecology; soil nitrogen cycling; ecology; agricultural soil management; bacterial and fungal communities; soil microplastic pollution and environmental effects; agricultural waste resource utilization

Special Issue Information

Dear Colleagues,

This Special Issue aims to understand the structure and function of soil microbial ecosystems, elucidating how soil environmental factors (such as soil physicochemical properties, nutrients and pollutants) influence the composition, diversity, and activity of the microbial community, and how microorganisms subsequently regulate soil health and ecosystem services. This research will enable the conservation of soil resources and the maintenance of ecological balance, and aid in guiding sustainable agriculture and addressing the challenge of global climate change.

Dr. Qin Qin
Dr. Jun Wang
Guest Editors

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Keywords

soil microbiology
microbial ecology
soil environment
soil physicochemical properties
microbial community
soil health
ecosystem functions
sustainable agriculture
climate change
pollutants

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Published Papers (5 papers)

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Research

24 pages, 3088 KB

Open AccessArticle

Comprehensive Evaluation of Biogas Slurry Fertility: A Study Based on the Effects of Biogas Slurry Irrigation on Soil Microorganisms and Enzyme Activities in Winter Wheat Fields

by Dongxue Yin, Jiajun Qin, Baozhong Wang, Dongdong Chen, Zhiguang Dai, Xiaoli Niu, Jie Zhu and Fengshun Zhang

Microorganisms 2025, 13(9), 2054; https://doi.org/10.3390/microorganisms13092054 - 4 Sep 2025

Viewed by 378

Abstract

This study evaluates the impact of using biogas slurry (BS) instead of nitrogen fertilizer (NF) on wheat soil, and aims to provide an optimized fertilization strategy for green wheat production. Five fertilization modes were tested: basal fertilizer only (CK), NF at the full-bearing stage (CF), BS at the jointing stage + NF at the grouting period (S1), NF at the jointing stage + BS at the grouting period (S2), and BS at the full-bearing stage (S3). Wheat yield in S3 treatment was not significantly different from CF (9632.57 kg·ha⁻¹), but significantly increased starch content by 23.39% (p < 0.05). Analysis of soil nutrient content showed that S3 treatment elevated ammonium nitrogen (AN) content by 98.30% during the harvest period and maintained the highest urease activity (686.45 μg·g⁻¹·d⁻¹). Microbial community analysis showed that the bacterial Shannon index under S3 treatment reached 7.09, and the abundance of Actinomycetes reached 39.40%. The fungal Simpson index was 0.02, lower than that of other treatments (p < 0.01). A comprehensive evaluation led to the conclusion that a complete replacement of BS with NF synergistically improves soil quick-acting nutrient levels, enhances soil enzyme activities, and sustains high microbial diversity, whilst maintaining wheat yield. Full article

(This article belongs to the Special Issue Soil Environment and Microorganisms)

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21 pages, 1893 KB

Open AccessArticle

Spatial Differentiation of Heavy Metals/Metalloids, Microbial Risk Genes and Soil Microbiota in a Sulfur-Contaminated Landscape

by Lina Li, Jiayin Zhao, Chang Liu, Yiyan Deng, Yunpeng Du, Yu Liu, Yuncheng Wu, Wenwei Wu and Xuejun Pan

Microorganisms 2025, 13(9), 2010; https://doi.org/10.3390/microorganisms13092010 - 28 Aug 2025

Viewed by 473

Abstract

Legacy sulfur smelting has left behind complex contamination landscapes, yet the spatial structuring of microbial risks and adaptation strategies across soil profiles remains insufficiently understood. Microbial risk genes, including those conferring resistance to antibiotic resistance (ARGs), biocide and metal resistance (BRGs/MRGs), and virulence (VFGs), are increasingly recognized as co-selected under heavy metal stress, posing both ecological and public health concerns. In this study, we integrated geochemical analyses with metagenomic sequencing and functional annotation to jointly characterize the vertical (0–7 m) and horizontal (~2 km) distribution of heavy metals/metalloids, microbial communities, and functional risk genes at a historic smelting site in Zhenxiong, Yunnan. Heavy metals and metalloids such as arsenic (As), chromium (Cr), copper (Cu), and lead (Pb) showed clear accumulation with depth, while significantly lower concentrations were observed in both upstream and downstream locations, revealing persistent vertical and horizontal pollution gradients. Correspondingly, resistance and virulence genes were co-enriched at contaminated sites, suggesting potential co-selection under prolonged stress. LEfSe analysis revealed distinct ecological patterns: vertically, upper layers were dominated by nutrient-cycling and mildly stress-tolerant taxa, while deeper layers favored metal-resistant, oligotrophic, and potentially pathogenic microorganisms; horizontally, beneficial and diverse microbes characterized low-contamination zones, whereas heavily polluted areas were dominated by resistant and stress-adapted genera. These findings provide new insights into microbial resilience and ecological risk under long-term smelting stress. Full article

(This article belongs to the Special Issue Soil Environment and Microorganisms)

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24 pages, 8045 KB

Open AccessArticle

Environmental Factors Drive the Changes of Bacterial Structure and Functional Diversity in Rhizosphere Soil of Hippophae rhamnoides subsp. sinensis Rousi in Arid Regions of Northwest China

by Pei Gao, Guisheng Ye, Siyu Guo, Yuhua Ma, Yongyi Zhang, Sixuan Sun, Lin Guo, Hongyuan San, Wenjie Liu, Qingcuo Ren, Shixia Wang and Renyuan Peng

Microorganisms 2025, 13(8), 1860; https://doi.org/10.3390/microorganisms13081860 - 8 Aug 2025

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Abstract

Hippophae rhamnoides subsp. sinensis Rousi has high ecological and medicinal value, and it is an important plant resource unique to the arid regions of Northwest China. Exploring the influence of climate characteristics and soil factors on the composition, diversity, and function of the rhizosphere bacterial community of Chinese seabuckthorn is of great value for developing and popularizing characteristic plant resources in the arid regions of Northwest China. In this study, the rhizosphere soil of 13 Chinese seabuckthorn distribution areas in the northwest of China was taken as the research object, the bacterial community map was constructed based on 16S rRNA gene high-throughput sequencing technology, and the species abundance composition, structural diversity, molecular co-occurrence network, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt), as well as the function of rhizosphere soil bacterial community, were systematically studied. Combined with Mantel test and redundancy analysis (RDA), the key habitat factors driving the rhizosphere soil bacterial community structure of Chinese seabuckthorn were explored. The results showed that: (1) The number of amplicon sequence variants (ASVs) in rhizosphere soil bacterial community of Chinese seabuckthorn was the highest in S2(3072) and the S12(3637), and the lowest in the S11(1358) and S13(1996). The rhizosphere soil bacterial community was primarily composed of Proteobacteria, Actinobacteriota, and Acidobacteriota. Except for the S6 and S11 habitats, the dominant bacterial genera were mainly Achromobacter, Acidobacter (RB41), and Sphingomonas. (2) The α and β diversity of rhizosphere soil bacterial communities of Chinese seabuckthorn across 13 distribution areas were significantly different. The number of operational taxonomic units (OTUs), Ace index, and Chao 1 index of soil bacterial community in the S12 distribution area are the highest, and they are the lowest in S11 distribution area, with significant differences. The aggregation of soil bacterial communities in the S5 and S10 distribution areas is the highest, while it is the lowest in the S6 and S11 distribution areas. (3) PICRUSt function classification of soil bacteria showed that Metabolism and Genetic Information Processing functions were the strongest across all distribution areas, with S10 exhibiting higher functional capacity than other areas and S11 showing the weakest. (4) Cluster analysis revealed that soil bacteria across the 13 distribution areas were clustered into two groups, with S10 and S12 distribution areas as one group (Group 1) and the remaining 11 distribution areas as another group (Group 2). (5) Redundancy analysis revealed that pH was the key soil environmental factor driving the rhizosphere soil bacterial community α-diversity of Chinese seabuckthorn, followed by altitude (ALT) and soil water content (SWC). In summary, Chinese seabuckthorn prefers neutral to alkaline soils, and environmental factors play an important role in driving bacterial diversity, community structure, functional profiles, and co-occurrence networks in rhizosphere soil of Chinese seabuckthorn. Full article

(This article belongs to the Special Issue Soil Environment and Microorganisms)

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14 pages, 2286 KB

Open AccessArticle

Seasonality and Vertical Structure of Microbial Communities in Alpine Wetlands

by Huiyuan Wang, Yue Li, Xiaoqin Yang, Bin Niu, Hongzhe Jiao, Ya Yang, Guoqiang Huang, Weiguo Hou and Gengxin Zhang

Microorganisms 2025, 13(5), 962; https://doi.org/10.3390/microorganisms13050962 - 23 Apr 2025

Cited by 1 | Viewed by 666

Abstract

The soil microbial community plays a crucial role in the elemental cycling and energy flow within wetland ecosystems. The temporal dynamics and spatial distribution of soil microbial communities are central topics in ecology. While numerous studies have focused on wetland microbial community structures at low altitudes, microbial diversity across seasons and depths and their environmental determinants remain poorly understudied. To test the seasonal variation in microbial communities with contrasting seasonal fluxes of greenhouse gases, a total of 36 soil samples were collected from different depths in the Namco wetland on the Tibetan Plateau across four seasons. We found significant seasonal variation in bacterial community composition, most pronounced in the Winter, but not in archaea. In particular, Proteobacteria decreased by 11.5% in Winter compared with other seasons (p < 0.05). The bacterial alpha diversity showed hump-shaped seasonal patterns with lower diversity in Winter, whereas archaea showed no significant patterns across depths. A PERMANOVA further revealed significant differences in the bacterial community structure between Winter and the other three seasons (p < 0.05). In addition, bacterial and archaeal community structures differed between surface (0–5 cm) and deeper (5–30 cm) soils (p < 0.01). Redundancy analysis showed that soil total nitrogen, soil total phosphorus, and total soil organic carbon significantly influenced bacteria and archaea (p < 0.05). Furthermore, soil moisture content and temperature strongly affected the bacterial community structure (p < 0.001). Our findings highlighted the seasonal variation in the microbial community and the profound influence of soil moisture and temperature on microbial structure in alpine wetlands on the Tibetan Plateau. Full article

(This article belongs to the Special Issue Soil Environment and Microorganisms)

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25 pages, 10349 KB

Open AccessArticle

Effects of Difenoconazole and Imidacloprid Seed Coatings on Soil Microbial Community Diversity and Ecological Function

by Dunfeng Feng, Jiabin Chen, Guo Li, Xiaoying Yang, Yujie Xiong, An Lao, Suzhen Huang and Zheng Zheng

Microorganisms 2025, 13(4), 806; https://doi.org/10.3390/microorganisms13040806 - 1 Apr 2025

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Abstract

Difenoconazole and imidacloprid are key components of seed-coating agents, which alter soil microbial community structure and function after application. Existing studies mainly focus on the environmental effects of their spraying application, while research on their impacts on the soil ecosystem when used as seed-coating agents is relatively limited. Through field experiments, this study systematically evaluated and compared the effects of difenoconazole and imidacloprid seed coatings on wheat rhizosphere soil microbial communities and ecological functions by measuring soil enzyme activities, employing 16S rRNA and ITS high-throughput sequencing technologies and predicting KEGG functional pathways. The results showed that imidacloprid and difenoconazole significantly reduced bacterial community diversity, particularly under the high-dosage difenoconazole treatment (0.18 g a.i./kg seed), with a 5.80% decrease in diversity by day 30. This treatment most strongly inhibited the phyla Bacteroidota and Myxococcota, with maximum reductions of 23.87% and 63.57%, respectively. However, the abundance of Actinobacteriota significantly increased, with a maximum increase of 38.53%. Additionally, fungal community diversity significantly increased under both difenoconazole and imidacloprid treatments. Both seed coatings significantly altered the microbial community structure from days 20 to 60, with recovery occurring by day 120. Furthermore, KEGG pathway analysis revealed that the high-dosage difenoconazole treatment (0.18 g a.i./kg seed) significantly activated functional pathways such as cell motility, signal transduction, and membrane transport, whereas the standard dosage (0.12 g a.i./kg seed) exhibited metabolic suppression. This study elucidates the dynamic impacts of seed-coating agent application on soil microbial communities, providing theoretical support for rational pesticide use and the optimization of agricultural strategies. Full article

(This article belongs to the Special Issue Soil Environment and Microorganisms)

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