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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 December 2025) | Viewed by 10699

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Prof. Dr. Zhiyong Li

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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, being vital for our 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 supposed 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 functional processes.

Here, we introduce this Special Issue, titled “State-of-the-Art Environmental Microbiology in China 2025”，which is the continuation of “State-of-the-Art Environmental Microbiology in China (2023–2024)” (https://www.mdpi.com/journal/microorganisms/special_issues/75S4KF6K98). It will be devoted to topics 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 250 words) can be sent to the Editorial Office for assessment.

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, and others
microbial pollution: pathogenic microorganisms in the environment (water/soil/air/food), microbial metabolism, environmental pollution (e.g., microbial toxin), and others
microbiological monitoring: testing method and monitoring technique development

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Published Papers (7 papers)

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Research

15 pages, 2274 KB

Open AccessArticle

Coupled Effects of Tree Species and Understory Morel on Modulating Soil Microbial Communities and Nutrient Dynamics

by Xia Yuan, Haiyan Qin, Yun Wang, Shuwen Wu, Zeyu Zhang, Muxin Fan, Li Li, Liuqian Tian and Yiwen Fu

Microorganisms 2026, 14(1), 99; https://doi.org/10.3390/microorganisms14010099 - 2 Jan 2026

Cited by 1 | Viewed by 534

Abstract

Morel mushrooms (Morchella spp.) are highly prized for their culinary and economic value. Understory cultivation, leveraging the symbiotic relationship between morels and trees, has gained increasing popularity. However, the effects of this practice on belowground microbial communities and nutrient dynamics remain poorly understood. In this study, we examined how understory cultivation of morels (Morchella sextelata) under five different tree species affects soil bacterial and fungal communities, as well as nutrient availability and mineral element content. The results revealed that soil physicochemical properties responded variably to morel cultivation under different tree species. Notably, understory morel cultivation reduced soil NO₃⁻-N by 38–67% across tree species, whereas NH₄⁺-N remained stable, reflecting the distinct nutrient preference of Morchella and associated trees, and suggesting targeted nitrate fertilization could mitigate nitrogen limitations. Understory cultivation significantly increased soil mineral elements, with Zelkova serrata (Z. serrata) showing the highest concentrations, elevating available potassium (AK), calcium (ECa), manganese (AMn) and boron (AB) by approximately 20%, 13%, 30%, and 168%, highlighting its potential for soil quality improvement. Microbial community composition was also significantly altered, with fungal communities exhibiting more pronounced shifts than bacterial communities, likely due to their closer ecological associations with morels. Importantly, Z. serrata markedly promoted microbial-mediated soil carbon and nitrogen accumulation, driven by mineral binding, root secretions and soil pH value. These findings enhance understanding of belowground effects of morel understory cultivation, revealing that select tree species like Z. serrata can improve soil quality and nutrient cycling, while targeted nitrate fertilization supports sustaining morel cultivation systems. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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16 pages, 20444 KB

Open AccessArticle

Plant-Mediated Soil Sickness: Steering the Rhizosphere into a Pathogenic Niche

by Jichao Li, Mingju Qi, Jinyu Zhang and Yingmei Zuo

Microorganisms 2026, 14(1), 52; https://doi.org/10.3390/microorganisms14010052 - 25 Dec 2025

Viewed by 535

Abstract

Continuous monoculture of Panax notoginseng leads to severe replant disease, yet the mechanisms by which root exudates mediate rhizosphere microbiome assembly and pathogen enrichment remain poorly understood. Here, we demonstrate that long-term root exudate accumulation acts as an ecological filter, driving the fungal community toward a phylogenetically impoverished, pathogen-dominated state. Specifically, exudates enriched the soil-borne pathogen Fusarium while reducing the abundance of potentially antagonistic fungi. In contrast, bacterial communities exhibited higher resilience, with exudates selectively enriching oligotrophic taxa such as Terrimonas and MND1, but suppressing nitrifying bacteria (e.g., Nitrospira) and plant-growth-promoting rhizobacteria (PGPR). Microbial functional profiling revealed a shift in nitrogen cycling, characterized by suppressed nitrification and enhanced nitrate reduction. Crucially, co-occurrence network analysis identified bacterial taxa strongly negatively correlated with Fusarium, providing a synthetic community blueprint for biocontrol strategies. Our study establishes a mechanistic link between root exudate accumulation and negative plant–soil feedback in monoculture systems, highlighting microbiome reprogramming as a key driver of replant disease. These insights offer novel avenues for manipulating rhizosphere microbiomes to sustain crop productivity in intensive agricultural systems. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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20 pages, 2171 KB

Open AccessArticle

by Lan Wang, Ciren Quzong, Sang-Gyal Skal, Chengwei Mu, Yaqin Zhao, Bo Fang, Yuan Zhang, Zhiyong Yang, Erping Hei, Xin Yuan and Tsechoe Dorji

Microorganisms 2025, 13(12), 2775; https://doi.org/10.3390/microorganisms13122775 - 5 Dec 2025

Cited by 1 | Viewed by 927

Abstract

The Beishan region near Shiquanhe Town in Ngari, western Xizang (Tibet), represents a typical alpine desert ecosystem on the Qinghai–Xizang Plateau. However, depth-related patterns of soil microbial communities and their physicochemical controls remain insufficiently understood. Here, microbial community composition and functional attributes were examined across three soil horizons—topsoil (0–20 cm), subsoil (20–40 cm), and deep subsoil (40–60 cm)—sampled in May 2024 prior to artificial greening. High-throughput 16S rRNA and ITS sequencing combined with physicochemical analyses revealed clear vertical stratification: bacteria were dominated by Proteobacteria and Actinobacteriota, and fungi by Ascomycota. Bacterial diversity was higher in the topsoil, whereas fungal diversity exhibited a gradual increase with soil depth; however, these trends did not reach statistical significance (p > 0.05). Functional predictions indicated predominantly aerobic heterotrophic bacteria and a shift from pathogenic to saprotrophic fungi with depth. Multivariate analyses (RDA, CCA, BRT) consistently identified soil pH and moisture as fundamental habitat constraints, and organic carbon, available phosphorus, and available potassium as physicochemical drivers with nonlinear threshold responses. These results highlight soil pH, moisture, and nutrient status (N, P, K) as primary determinants of microbial community assembly and provide guidance for microbially informed ecological restoration in alpine desert ecosystems. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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26 pages, 8002 KB

Open AccessArticle

Functional Genomic Characteristics of Marine Sponge-Associated Microbulbifer spongiae MI-G^T

by Nabila Ishaq, Qianqian Song, Micha Ilan and Zhiyong Li

Microorganisms 2025, 13(8), 1940; https://doi.org/10.3390/microorganisms13081940 - 20 Aug 2025

Cited by 1 | Viewed by 1190

Abstract

The genus Microbulbifer comprises a group of marine, gram-negative bacteria known for their remarkable ability to adapt to a variety of environments. Therefore, this study aimed to investigate the genetic diversity and metabolic characteristics of M. spongiae MI-G^T and three Microbulbifer reference strains by genomic and comparative genomic analysis. Compared to free-living reference strains, the lower GC content, higher number of strain-specific genes, pseudogenes, unique paralogs, dispensable genes, and mobile gene elements (MGEs) such as genomic islands (GIs) and insertion sequence (IS) elements, while the least number of CAZymes, indicates that M. spongiae MI-G^T may be a facultative sponge-symbiont. Comparative genomic analysis indicates that M. spongiae MI-G^T possesses a plasmid and a higher number of strain-specific genes than Microbulbifer reference strains, showing that M. spongiae MI-G^T may have acquired unique genes to adapt sponge-host environment. Moreover, there are differences in the functional distribution of genes belonging to different COG-classes in four Microbulbifer strains. COG-functional analysis reveals a lower number of strain-specific genes associated with metabolism, energy production, and motility in M. spongiae MI-G^T compared to Microbulbifer reference strains, suggesting that sponge-associated lifestyle may force this bacterium to acquire nutrients from the sponge host and loss motility genes. Finally, we found that several proteins associated with oxidative stress response (sodC, katA, catA, bcp, trmH, cspA), osmotic stress response (dsbG, ampG, amiD_2, czcA, czcB, and corA), and tolerance to biotoxic metal proteins (dsbG, ampG, amiD_2, czcA, czcB, and corA) are absent in M. spongiae MI-G^T but present in Microbulbifer reference strains, indicating that M. spongiae MI-G^T live in a stable and less stress environment provided by the sponge host than free-living Microbulbifer strains. Our results suggest M. spongiae MI-G^T exhibits gene characteristics related to its adaptation to the sponge host habitat, meanwhile reflecting its evolution towards a sponge-associated lifestyle. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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19 pages, 2310 KB

Open AccessArticle

Ecosystem Multifunctionality Regulated by Soil Microbial Activity and Indicator Taxa Versus Biodiversity for Industrial Solar Facilities on the Qinghai–Tibet Plateau

by Yu Liu, Chengxiang Ding, Tiemei Wang, Derong Su, Zhuoqing Li, Chaoyang Feng and Zhanjun Quan

Microorganisms 2025, 13(7), 1464; https://doi.org/10.3390/microorganisms13071464 - 24 Jun 2025

Cited by 1 | Viewed by 1257

Abstract

The drive towards carbon neutrality has prompted the worldwide expansion of utility-scale solar facilities. Previous studies have reported the positive effects of solar facilities’ installation on pasture productivity and biodiversity in arid regions. However, our understanding of how solar facilities influence a wide range of ecosystem functions simultaneously, and the relative contributions of soil microbial attributes, remains incomplete. To address this gap, we assessed the changes in ecosystem multifunctionality following solar facility installation in an alpine desert grassland in the Qinghai–Tibet plateau by measuring twenty-three ecosystem function indicators comprising primary production, the soil nutrient pool, carbon cycling, nitrogen cycling, phosphorus cycling and oxidation–reduction. Furthermore, we estimated the soil microbial diversity, microbial indicator taxa and microbial activity to identify the primary driving factors. The results showed that solar facilities had positive effects on ecosystem multifunctionality; the positive effect size was higher in the initial installation period (31.4%) than in the constant running period (3.5%). The enhancements in ecosystem multifunctionality were mainly due to enhanced nutrient cycling induced by the increased abundance of fungal indicator taxa and microbial activity. Moreover, the structural equation model revealed distinct regulatory paths between the two periods and a transition in the primary driving factors of ecosystem multifunctionality from microbial indicator taxa to microbial activity. In conclusion, our study demonstrates the positive influence of solar facilities on multiple ecosystem functions, emphasizing the critical role of soil microbial mechanisms in regulating ecosystem multifunctionality. These findings provide valuable insights into soil biota-driven processes that could inform strategies aimed at enhancing soil health and ecosystem functionality in arid grasslands under human-managed systems. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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17 pages, 2927 KB

Open AccessArticle

Multitrophic and Multidimensional Insights into Biodiversity and Functional Trait Responses to Precipitation Changes in Alpine Grasslands

by Yu Liu, Chengxiang Ding and Zhanjun Quan

Microorganisms 2025, 13(5), 1011; https://doi.org/10.3390/microorganisms13051011 - 28 Apr 2025

Viewed by 1505

Abstract

Biodiversity and functional traits are increasingly recognized as pivotal factors in regulating ecosystem functioning and stability. However, the patterns and processes of multidimensional biodiversity and functional traits along environmental gradients remain insufficiently understood. In this study, we examined taxonomic, phylogenetic, and functional diversity across multiple trophic levels in 38 alpine grassland sites along a precipitation gradient on the Qinghai–Tibet Plateau. Our findings reveal asynchronous responses of taxonomic, phylogenetic, and functional diversity metrics, as well as functional traits across trophic levels, to variations in precipitation. Soil microbial diversity and functional traits exhibited stronger responses to precipitation changes compared to plant communities, with a tighter coupling observed between microbial diversity and microbial functional traits. Climate and soil properties jointly regulated diversity and functional trait metrics, with the climate exerting greater influence on functional traits and soil properties playing a dominant role in shaping diversity patterns. This study highlights the distinct responses of biodiversity and functional trait attributes to environmental shifts, emphasizing the importance of integrating multidimensional and multitrophic perspectives to advance our understanding of community assembly processes. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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23 pages, 7087 KB

Open AccessArticle

Enhanced Leaching of Lepidolite by Acidophilic Microorganisms Under Mechanical Activation

by Jingna Li, Mengyuan Wang, Ruiyong Zhang, Hongchang Liu, Shiyun Huang, Yang Liu, Rui Liao, Arevik Vardanyan, Jinlan Xia and Jun Wang

Microorganisms 2025, 13(2), 415; https://doi.org/10.3390/microorganisms13020415 - 13 Feb 2025

Cited by 3 | Viewed by 1959

Abstract

In recent years, mechanical activation technology has been extensively applied as a pretreatment process to increase the leaching efficiency in hydrometallurgical mineral processing. However, studies on its application in the lepidolite bioleaching process are limited. Therefore, the effects of mechanical activation on lithium extraction by an acidophilic iron/sulfur-oxidizing microbial community under different nutrient conditions were evaluated in this study. The solution behavior, phase morphology, and compositional evolution, and microbial community structure succession under eutrophic conditions with exogenous pyrite as the energy substrate and oligotrophic conditions, were investigated. The results revealed that mechanical activation significantly influences the microbial community structure and the interrelationship between microbial activity and mineral phase decomposition and transformation by altering the physical and chemical properties of lepidolite. The best leaching effect was observed in the eutrophic bioleaching groups, followed by the oligotrophic groups at all mechanical activation times. Notably, at a rotation speed of 200 r/min, a material-to-ball mass ratio of 1:20, and an activation time of 150 min, the maximum leaching rates of lithium under eutrophic and oligotrophic conditions were 24.9% and 20.8%, respectively, which were 20.0% and 17.9% higher than those of the nonactivated group. The phase and composition analyses indicated that the dissolution of lithium silicate minerals occurs through a combination of protic acid corrosion, the complexation/electrostatic interactions of extracellular polymeric substances, and the complexation of secondary minerals. These results indicate that the leaching effect is closely related to the pretreatment of mechanical activation, the energy substrates, and the microbial community structure, and this has important reference value for the optimization of the bioleaching process of lepidolite. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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