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Microorganisms
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State-of-the-Art Environmental Microbiology in China 2026
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State-of-the-Art Environmental Microbiology in China 2026

A Special Issue of Microorganisms (ISSN 2076-2607) belonging to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 2285

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, 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 2026”，which is the continuation of “State-of-the-Art Environmental Microbiology in China (2023–2024)”, https://www.mdpi.com/journal/microorganisms/special_issues/75S4KF6K98, and the Special Issue “State-of-the-Art Environmental Microbiology in China 2025”, https://www.mdpi.com/journal/microorganisms/special_issues/BW9CTAS1UJ. 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.

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-anonymized 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 (3 papers)

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16 pages, 8876 KB  
Article
Coral Mucus Microbial Community Change and Resistant Strategy Under UV Radiation: A Case from Porites sp. and Favites sp. Mucus Microbiome
by Tianxiang Guo, Qun Jiang, Yaxing Liu, Chuanliang Wu and Zhiyong Li
Microorganisms 2026, 14(6), 1296; https://doi.org/10.3390/microorganisms14061296 - 9 Jun 2026
Viewed by 475
Abstract
Coral mucus serves as a crucial defensive barrier for corals, where the mucus microbes play a vital role in the coral’s resistance to external stresses. However, detailed knowledge of the effect of UV radiation on coral mucus microbiome is limited, particularly regarding the [...] Read more.
Coral mucus serves as a crucial defensive barrier for corals, where the mucus microbes play a vital role in the coral’s resistance to external stresses. However, detailed knowledge of the effect of UV radiation on coral mucus microbiome is limited, particularly regarding the UV resistance mechanisms of coral mucus microbes. This study investigates changes in the mucus microbial community and possible UV-resistant mechanisms of the mucus microbiota of Porites sp. and Favites sp. under UV stress using high-throughput sequencing, UV-resistant microbial isolation, and RT-qPCR analysis. Compared to the control, UV stress alters microbial community structure by reducing microbial diversity, e.g., the relative abundance of Aquibacter, Agaribacter, and Oleibacter in coral Porites sp., and the Roseobacter clade CHAB_I_5 lineage, Roseivirga, and Nautella in coral Favites sp. increase under UV stress. Meanwhile, it is indicated that the Favites sp. mucus microbiome is much more sensitive than the Porites sp. mucus microbiome. A total of 428 microbial strains belonging to 5 phyla, 7 classes, 15 orders, 23 families, and 47 genera were isolated from these two coral mucus species, with Ruegeria and Rossellomorea as the most abundant cultured taxa. Pseudoalteromonas galatheae strain P12 and Limimaricola pyoseonensis strains P2 and P9 have been proven to exhibit higher UV resistance by enhanced expression of tyr, sod, gogat, and uvrC genes, indicating that the UV resistance of coral mucus bacteria involves complex molecular processes, including upregulation of antioxidant enzyme expression and enhancement of melanin and glutamic acid biosynthesis. These findings enhance our understanding of coral mucus microbial ecological functions, particularly highlighting the coral mucus microbial UV resistance strategy. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2026)
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18 pages, 2044 KB  
Article
Herbicide Application Under Co-Cultivation Is Associated with Early Microbiome Assembly Shifts and Later Physiological Decline in Rice
by Yingxi Li, Mingfeng He, Yao Song, Lu Liu, Jiling Xiao, Jie Wang, Bin Yang, Shunyi Ouyang, Xin Li, Di Peng and Zheyuan Zhu
Microorganisms 2026, 14(5), 1137; https://doi.org/10.3390/microorganisms14051137 - 17 May 2026
Viewed by 626
Abstract
Herbicides considered selective to rice are generally evaluated based on their direct crop safety and weed suppression effects, yet it remains unclear whether they may also trigger indirect or context-dependent effects on rice under rice–barnyardgrass co-cultivation. To address this question, we compared rice [...] Read more.
Herbicides considered selective to rice are generally evaluated based on their direct crop safety and weed suppression effects, yet it remains unclear whether they may also trigger indirect or context-dependent effects on rice under rice–barnyardgrass co-cultivation. To address this question, we compared rice performance and associated microbial dynamics under six conditions: rice–barnyardgrass co-cultivation and rice monoculture, each treated with a water spray control or sublethal doses of propanil (Pro, 66.7 mg a.i. L−1) or cyhalofop-butyl (Cyh, 5.86 mg a.i. L−1). Barnyardgrass exhibited visible injury and stronger leaf-level oxidative stress responses, whereas rice displayed no discernible phytotoxic symptoms. Nevertheless, under co-cultivation, herbicide treatment significantly suppressed rice growth, with up to 17.8% lower root lengths and 24.8% lower shoot fresh weights, with reductions varying by herbicide and trait. By contrast, comparable suppression was not observed under herbicide exposure or co-cultivation alone, identifying this response as an emergent, context-dependent negative effect. Microbiota reassembly emerged as an early and stage-specific component of the herbicide-associated response under co-cultivation, with the most pronounced changes detected on day 5 and occurring primarily in bacterial communities. Moreover, bacterial community variation was negatively correlated with root length (ρ = −0.664), and urease activity declined under herbicide treatment. Together, these findings indicate that in paddy fields, herbicides act not only on individual plants but also as an external disturbance to the coupled rice–barnyardgrass system, for which microbiota reorganization represents a key component of the ecological response. Our results suggest that herbicide selectivity should be interpreted within a crop–weed–microbiome context, rather than being inferred solely from their direct crop safety and weed suppression effects. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2026)
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Other

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29 pages, 4860 KB  
Systematic Review
A Multidimensional Bibliometric Analysis of Research Hotspots and Development Trends in Functional Microorganisms of the Genus Geobacter
by Lisi Jiang, Jianing Zhang, Chenxu Wang, Junying Wu, Wenyuan Li, Jiajun Fan, Lixin Guo, Chang Guo and Yang Zhang
Microorganisms 2026, 14(8), 1678; https://doi.org/10.3390/microorganisms14081678 - 31 Jul 2026
Viewed by 419
Abstract
Rapid industrialization, urbanization, resource exploitation, and energy use have caused global pollution and ecological degradation, hindering sustainable development. Functionally versatile microbes are eco-friendly resources for addressing environmental problems. Geobacter, a vital genus featuring outstanding extracellular electron transfer (EET), has drawn widespread research [...] Read more.
Rapid industrialization, urbanization, resource exploitation, and energy use have caused global pollution and ecological degradation, hindering sustainable development. Functionally versatile microbes are eco-friendly resources for addressing environmental problems. Geobacter, a vital genus featuring outstanding extracellular electron transfer (EET), has drawn widespread research interest, with studies centered on EET mechanisms, microbial fuel cells, biogeochemical cycling and environmental bioremediation. Though valuable across energy, environmental and geoscience disciplines, a systematic bibliometric review of Geobacter research evolution is absent. This paper fills the gap via comprehensive bibliometric analysis of 2000–2026 Web of Science Core Collection papers covering Geobacter and the closely related genus Trichlorobacter, recently re-established as a standalone genus, focusing on bioremediation, dissimilatory Fe(III) reduction, microbial electrochemistry and biogeochemical cycles. This bibliometric profiling clarifies the evolving research frontiers in electroactive microbe-mediated environmental remediation and geochemical cycling, delivering refined scientific implications and actionable theoretical guidance for future ecological restoration and pollution remediation practices. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2026)
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