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Microorganisms
Special Issues
State-of-the-Art Environmental Microbiology in China (2023–2024)
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State-of-the-Art Environmental Microbiology in China (2023–2024)

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 18255

Special Issue Editor

Prof. Dr. Zhiyong Li

E-Mail Website
Guest Editor
State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: sponge/coral-microbes symbioses; marine microbiome; marine natural products
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial communities are responsible for energy and nutrient cycling, and are massively involved in the planet’s sustainability. Microbes are directly involved in the dynamics of climate change through their impact on the destabilization, mineralization and sequestration of organic matter. The facets of microbial diversity consist of morphological, structural, metabolic, ecological or evolutionary diversity; however, the central question in microbial ecology—“Who eats what, where and when?”—queries how the key player in the community is to perform the most meaningful activity. To answer this, one major task is to identify the relationships between the composition of the microbial community and the functional processes.

Here, we introduce the Special Issue “State-of-the-Art Environmental Microbiology in China (2023–2024)”. This Special Issue will be devoted to topics that remain focused on the study of microbial processes in the environment, microbial communities and microbial interactions, including omics technologies and cross-disciplinary studies dedicated to basic and/or applied research in China. The editorial board will review all manuscripts submitted for publication in this section.

Prof. Dr. Zhiyong Li
Guest Editor

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

  • structure and function of microbial communities
  • microbial community genetics, transcriptomics, proteomics and metabolomics
  • microbial interaction
  • microbial communication
  • microbial ecology
  • microbial population biology
  • biogeochemical processes (C, N, P, S cycles)
  • microbial life in extreme environments
  • evolutionary processes of microbial communities
  • biofilm formation and the surfaces of microbes
  • metabolic flux analysis and stable isotope probing (DNA, RNA and protein)
  • microbiome biology of environmental habitats (e.g., soil, rhizosphere or aquifer)
  • microbial treatment: microbial biodegradation, microbial bioremediation, microbial and waste recycling, microbial pesticide, microbial fertilizer, etc.
  • microbial pollution: pathogenic microorganisms in the environment (water/soil/air/food), microbial metabolism and environmental pollution (e.g., microbial toxin), etc.
  • microbiological monitoring: testing method and monitoring technique development

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Published Papers (10 papers)

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Research

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17 pages, 10271 KiB  
Article
Seasonal Dynamics of Eukaryotic Microbial Communities in the Water-Receiving Reservoir of the Long-Distance Water Diversion Project, China
by Yingying Yang, Fangfang Ci, Ailing Xu, Xijian Zhang, Ning Ding, Nianxin Wan, Yuanyuan Lv and Zhiwen Song
Microorganisms 2024, 12(9), 1873; https://doi.org/10.3390/microorganisms12091873 - 11 Sep 2024
Viewed by 473
Abstract
Inter-basin water transfer projects, such as the Yellow River to Qingdao Water Diversion Project (YQWD), are essential for addressing water scarcity, but impact local aquatic ecosystems. This study investigates the seasonal characteristics of eukaryotic microbial communities in the Jihongtan Reservoir, the main water-receiving [...] Read more.
Inter-basin water transfer projects, such as the Yellow River to Qingdao Water Diversion Project (YQWD), are essential for addressing water scarcity, but impact local aquatic ecosystems. This study investigates the seasonal characteristics of eukaryotic microbial communities in the Jihongtan Reservoir, the main water-receiving body of YQWD, over a one-year period using 18S rDNA amplicon sequencing. The results showed that the eukaryotic microbial diversity did not exhibit significant seasonal variation (p > 0.05), but there was a notable variance in the community structure (p < 0.05). Arthropoda and Paracyclopina, representing the most dominant phylum and the most dominant genus, respectively, both exhibited the lowest abundance during the winter. The Chlorophyta, as the second-dominant phylum, demonstrates its higher abundance in the spring and winter. The Mantel test and PLS-PM (Partial Least Squares Path Modeling) revealed that water temperature (WT), dissolved oxygen (DO), and pH influenced the seasonal dynamic of eukaryotic microbial communities significantly, of which WT was the primary driving factor. In addition to environmental factors, water diversion is likely to be an important influencing factor. The results of the co-occurrence network and robustness suggested that the spring network is the most complex and exhibits the highest stability. Moreover, keystone taxa within networks have been identified, revealing that these key groups encompass both abundant and rare species, with specificity to different seasons. These insights are vital for understanding the seasonal variation of microbial communities in the Jihongtan Reservoir during ongoing water diversions. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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16 pages, 3505 KiB  
Article
Effects of Long-Term Application of Nitrogen Fertilizer on Soil Acidification and Biological Properties in China: A Meta-Analysis
by Liqiang Zhang, Zehang Zhao, Bailing Jiang, Bate Baoyin, Zhengguo Cui, Hongyu Wang, Qiuzhu Li and Jinhu Cui
Microorganisms 2024, 12(8), 1683; https://doi.org/10.3390/microorganisms12081683 - 15 Aug 2024
Viewed by 1574
Abstract
Soil acidification is a global environmental problem with significant impacts on agricultural production, environmental protection, and ecosystem health. Soil acidification is widespread in China, affecting crop yields, agricultural product quality, and biodiversity. Since the 1980s, much work has been done on acidic soils [...] Read more.
Soil acidification is a global environmental problem with significant impacts on agricultural production, environmental protection, and ecosystem health. Soil acidification is widespread in China, affecting crop yields, agricultural product quality, and biodiversity. Since the 1980s, much work has been done on acidic soils in China, but it is controversial whether excessive nitrogen fertilizer application can lead to soil acidification mechanisms. To address the above issues, we conducted a meta-analysis of 115 published papers to integrate and analyze the effects of N fertilizer application on soil acidification and biological properties from 1980 to 2024. We also quantified the effect of nitrogen fertilization on soil acidification and biological changes under different climatic conditions. The results showed that under long-term application of nitrogen fertilizers in China from 1980 to 2024, soil pH decreased by an average of 15.27%, and the activities of soil urease, nitrate reductase, nitrite reductase, catalase, glutamate dehydrogenase, and glutamate synthetase decreased by an average of 9.82–22.37%. The soil microbial community richness (Chao1 index) increased by 6.53%, but the community diversity (Shannon index) decreased by 15.42%. Among the dominant soil microorganisms, the relative abundance of bacteria decreased by an average of 9.67–29.38% and the abundance of gene expression of nifH, amoA-AOA, amoA-AOB, and qnorB decreased by 9.92–19.83%. In addition, we found that the mean annual temperature and rainfall impacted soil acidification via their effect on soil microbial diversity and community composition. This study provides a scientific basis for an in-depth understanding of the spatial and temporal variation of soil acidification and biological properties in China. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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18 pages, 7706 KiB  
Article
Maize–Soybean Rotation and Intercropping Increase Maize Yield by Influencing the Structure and Function of Rhizosphere Soil Fungal Communities
by Liqiang Zhang, Yuhan Yang, Zehang Zhao, Yudi Feng, Baoyin Bate, Hongyu Wang, Qiuzhu Li and Jinhu Cui
Microorganisms 2024, 12(8), 1620; https://doi.org/10.3390/microorganisms12081620 - 8 Aug 2024
Viewed by 785
Abstract
Soil-borne diseases are exacerbated by continuous cropping and negatively impact maize health and yields. We conducted a long-term (11-year) field experiment in the black soil region of Northeast China to analyze the effects of different cropping systems on maize yield and rhizosphere soil [...] Read more.
Soil-borne diseases are exacerbated by continuous cropping and negatively impact maize health and yields. We conducted a long-term (11-year) field experiment in the black soil region of Northeast China to analyze the effects of different cropping systems on maize yield and rhizosphere soil fungal community structure and function. The experiment included three cropping systems: continuous maize cropping (CMC), maize–soybean rotation (MSR), and maize–soybean intercropping (MSI). MSI and MSR resulted in a 3.30–16.26% lower ear height coefficient and a 7.43–12.37% higher maize yield compared to CMC. The richness and diversity of rhizosphere soil fungi were 7.75–20.26% lower in MSI and MSR than in CMC. The relative abundances of Tausonia and Mortierella were associated with increased maize yield, whereas the relative abundance of Solicoccozyma was associated with decreased maize yield. MSI and MSR had higher proportions of wood saprotrophs and lower proportions of plant pathogens than CMC. Furthermore, our findings indicate that crop rotation is more effective than intercropping for enhancing maize yield and mitigating soil-borne diseases in the black soil zone of Northeast China. This study offers valuable insights for the development of sustainable agroecosystems. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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19 pages, 6109 KiB  
Article
Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication
by Zhen Xie, Wei Li, Kaiwen Yang, Xinze Wang, Shunzi Xiong and Xiaojun Zhang
Microorganisms 2024, 12(8), 1617; https://doi.org/10.3390/microorganisms12081617 - 8 Aug 2024
Viewed by 682
Abstract
The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of [...] Read more.
The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan–Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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17 pages, 3730 KiB  
Article
Biodegradation of Crude Oil by Nitrate-Reducing, Sulfate-Reducing, and Methanogenic Microbial Communities under High-Pressure Conditions
by Lu Wang, Yong Nie, Xinglong Chen, Jinbo Xu, Zemin Ji, Wenfeng Song, Xiaofang Wei, Xinmin Song and Xiao-Lei Wu
Microorganisms 2024, 12(8), 1543; https://doi.org/10.3390/microorganisms12081543 - 27 Jul 2024
Viewed by 1021
Abstract
Carbon capture, utilization, and storage (CCUS) is an important component in many national net-zero strategies, and ensuring that CO2 can be safely and economically stored in geological systems is critical. Recent discoveries have shown that microbial processes (e.g., methanogenesis) can modify fluid [...] Read more.
Carbon capture, utilization, and storage (CCUS) is an important component in many national net-zero strategies, and ensuring that CO2 can be safely and economically stored in geological systems is critical. Recent discoveries have shown that microbial processes (e.g., methanogenesis) can modify fluid composition and fluid dynamics within the storage reservoir. Oil reservoirs are under high pressure, but the influence of pressure on the petroleum microbial community has been previously overlooked. To better understand microbial community dynamics in deep oil reservoirs, we designed an experiment to examine the effect of high pressure (12 megapascals [MPa], 60 °C) on nitrate-reducing, sulfate-reducing, and methanogenic enrichment cultures. Cultures were exposed to these conditions for 90 d and compared with a control exposed to atmospheric pressure (0.1 MPa, 60 °C). The degradation characteristic oil compounds were confirmed by thin-layer analysis of oil SARA (saturates, aromatics, resins, and asphaltenes) family component rods. We found that the asphaltene component in crude oil was biodegraded under high pressure, but the concentration of asphaltenes increased under atmospheric pressure. Gas chromatography analyses of saturates showed that short-chain saturates (C8–C12) were biodegraded under high and atmospheric pressure, especially in the methanogenic enrichment culture under high pressure (the ratio of change was −81%), resulting in an increased relative abundance of medium- and long-chain saturates. In the nitrate-reducing and sulfate-reducing enrichment cultures, long-chain saturates (C22–C32) were biodegraded in cultures exposed to high-pressure and anaerobic conditions, with a ratio of change of −8.0% and −2.3%, respectively. However, the relative proportion of long-chain saturates (C22–C32) increased under atmospheric pressure. Gas Chromatography Mass Spectrometry analyses of aromatics showed that several naphthalene series compounds (naphthalene, C1-naphthalene, and C2-naphthalene) were biodegraded in the sulfate-reducing enrichment under both atmospheric pressure and high pressure. Our study has discerned the linkages between the biodegradation characteristics of crude oil and pressures, which is important for the future application of bioenergy with CCUS (bio-CCUS). Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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9 pages, 1151 KiB  
Communication
Biogenic Phosphonate Utilization by Globally Distributed Diatom Thalassiosira pseudonana
by Huilin Shu, Yuan Shen, Hongwei Wang, Xueqiong Sun, Jian Ma and Xin Lin
Microorganisms 2024, 12(4), 761; https://doi.org/10.3390/microorganisms12040761 - 10 Apr 2024
Viewed by 1128
Abstract
Phosphonates are a class of organic phosphorus (P) compounds that contribute ~25% of dissolved organic P. Recent studies reveal the important role of phosphonates mediated by prokaryotes in the marine P redox cycle. However, its bioavailability by eukaryotic phytoplankton is under debate. 2-Aminoethylphosphonic [...] Read more.
Phosphonates are a class of organic phosphorus (P) compounds that contribute ~25% of dissolved organic P. Recent studies reveal the important role of phosphonates mediated by prokaryotes in the marine P redox cycle. However, its bioavailability by eukaryotic phytoplankton is under debate. 2-Aminoethylphosphonic acid (2-AEP) and 2-amino-3-phosphonopropionic acid (2-AP3) are two biogenic phosphonates in the marine environment. Here, Thalassiosira pseudonana, a common diatom species in the ocean, is able to recover growth from P starvation when provided with 2-AEP and 2-AP3. Moreover, 2-AEP cultures exhibited a more similar growth rate at 12 °C than at 25 °C when compared with inorganic P cultures. The cellular stoichiometry of 2-AEP groups was further determined, the values of which are in-between the P-depleted and DIP-replete cultures. This study provides evidence that biogenic phosphonates could be adopted as alternative P sources to support diatom growth and may provide physiological adaptation. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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19 pages, 8145 KiB  
Article
Driving Factors Influencing Soil Microbial Community Succession of Coal Mining Subsidence Areas during Natural Recovery in Inner Mongolia Grasslands
by Dongqiang Lu, Zhen Mao, Yan Tang, Bo Feng and Liang Xu
Microorganisms 2024, 12(1), 87; https://doi.org/10.3390/microorganisms12010087 - 31 Dec 2023
Cited by 2 | Viewed by 1357
Abstract
Soil microorganisms significantly influence the energy flow and material cycle of soil ecosystems, making them highly susceptible to environmental changes, such as those induced by mining activities. Studying the succession of soil microbial communities after mining subsidence is crucial for comprehending the significance [...] Read more.
Soil microorganisms significantly influence the energy flow and material cycle of soil ecosystems, making them highly susceptible to environmental changes, such as those induced by mining activities. Studying the succession of soil microbial communities after mining subsidence is crucial for comprehending the significance of soil microbes in the natural recovery process following subsidence. Therefore, the soil properties, vegetation communities, and soil microbial communities of the subsidence area, as well as unexploited areas, were analyzed during the natural restoration process (1, 2, 5, 10, and 15 years). The results demonstrate that mining subsidence has a significant impact on the aboveground vegetation community, soil properties, and microbiological community. Following an extended period of natural recovery, a new stable state has emerged, which differs from that observed in non-subsidence areas. The total nitrogen, nitrate nitrogen, and ammonium nitrogen amounts may be key factors driving the natural recovery of bacterial communities, and total potassium and available potassium may be key factors driving the natural recovery of fungal communities. The natural recovery mechanism of soil microorganisms was analyzed along with the changes related to vegetation and soil physicochemical properties. The mechanism was explained from three perspectives, namely, plant-led, soil-led, and soil-microbial-led, which could provide a theoretical basis for the natural restoration of grassland ecosystems and provide guidance for the treatment of coal mining subsidence areas. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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18 pages, 4915 KiB  
Article
The Impact and Determinants of Mountainous Topographical Factors on Soil Microbial Community Characteristics
by Jiantao Yu, Suyan Li, Xiangyang Sun, Wenzhi Zhou, Libing He, Guanyu Zhao, Zhe Chen, Xueting Bai and Jinshuo Zhang
Microorganisms 2023, 11(12), 2878; https://doi.org/10.3390/microorganisms11122878 - 28 Nov 2023
Cited by 1 | Viewed by 1322
Abstract
Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation [...] Read more.
Soil bacterial and fungal community communities play significant ecological functions in mountain ecosystems. However, it is not clear how topographic factors and soil physicochemical properties influence changes in microbial community structure and diversity. This study aims to investigate how altitude and slope orientation affect soil physicochemical properties, soil microbial communities, and their contributing factors. The assessment was conducted using Illumina MiSeq sequencing in various altitude gradients and on slopes with different aspects (shady slopes and sunny slopes) in the subalpine meadow of Dongling Mountain, Beijing. Topographical factors had a significant effect on soil physicochemical properties: the primary factors determining the structure of microbial communities are total potassium (TK), ammonium nitrogen (NH4+-N), and soil organic carbon (SOC). There was no significant change in the diversity of the bacterial community, whereas the diversity of the fungal community displayed a single-peaked trend. The effect of slope orientation on microbial communities was not as significant as the effect of elevation on them. The number of bacterial communities with significant differences showed a unimodal trend, while the number of fungal communities showed a decreasing trend. The co-occurrence network of fungal communities exhibits greater intricacy than that of bacterial communities, and bacterial communities are more complex in soils with sunny slopes compared to soils with shady slopes, and the opposite is true for fungal communities. The identification of the main factors that control soil microbial diversity and composition in this study, provided the groundwork for investigating the soil microbial response and adaptation to environmental changes in subalpine meadows. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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17 pages, 5321 KiB  
Article
The Salinity Survival Strategy of Chenopodium quinoa: Investigating Microbial Community Shifts and Nitrogen Cycling in Saline Soils
by Xuli Zhao, Tianzhu Meng, Shenghan Jin, Kaixing Ren, Zhe Cai, Bo Cai and Saibao Li
Microorganisms 2023, 11(12), 2829; https://doi.org/10.3390/microorganisms11122829 - 21 Nov 2023
Cited by 2 | Viewed by 1322
Abstract
Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the [...] Read more.
Quinoa is extensively cultivated for its nutritional value, and its exceptional capacity to endure elevated salt levels presents a promising resolution to the agricultural quandaries posed by salinity stress. However, limited research has been dedicated to elucidating the correlation between alterations in the salinity soil microbial community and nitrogen transformations. To scrutinize the underlying mechanisms behind quinoa’s salt tolerance, we assessed the changes in microbial community structure and the abundance of nitrogen transformation genes across three distinct salinity thresholds (1 g·kg−1, 3 g·kg−1, and 6 g·kg−1) at two distinct time points (35 and 70 days). The results showed the positive effect of quinoa on the soil microbial community structure, including changes in key populations and its regulatory role in soil nitrogen cycling under salt stress. Choroflexi, Acidobacteriota, and Myxococcota were inhibited by increased salinity, while the relative abundance of Bacteroidota increased. Proteobacteria and Actinobacteria showed relatively stable abundances across time and salinity levels. Quinoa possesses the ability to synthesize or modify the composition of keystone species or promote the establishment of highly complex microbial networks (modularity index > 0.4) to cope with fluctuations in external salt stress environments. Furthermore, quinoa exhibited nitrogen (N) cycling by downregulating denitrification genes (nirS, nosZ), upregulating nitrification genes (Archaeal amoA (AOA), Bacterial amoA (AOB)), and stabilizing nitrogen fixation genes (nifH) to absorb nitrate–nitrogen (NO3−_N). This study paves the way for future research on regulating quinoa, promoting soil microbial communities, and nitrogen transformation in saline environments. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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Review

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22 pages, 4527 KiB  
Review
Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects
by Lin Pan and Baiyan Cai
Microorganisms 2023, 11(12), 2904; https://doi.org/10.3390/microorganisms11122904 - 1 Dec 2023
Cited by 17 | Viewed by 6503
Abstract
Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42− and H2PO [...] Read more.
Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42− and H2PO4−, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400–1000 mg/kg, of which only 1.00–2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China (2023–2024))
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