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: 30 June 2024 | Viewed by 5997

Special Issue Editor


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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
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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

Published Papers (5 papers)

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Research

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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 470
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
Viewed by 773
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
Viewed by 854
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
Viewed by 782
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 - 01 Dec 2023
Cited by 6 | Viewed by 2557
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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