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Microorganisms
Special Issues
Advances in Genomics and Ecology of Environmental Microorganisms
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Advances in Genomics and Ecology of Environmental Microorganisms

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 579

Special Issue Editor

Dr. Renxing Liang

E-Mail Website
Guest Editor
State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
Interests: deep earth microbial diversity and biogeochemical cycles; permafrost microbes and global change; paleomicrobiome and environmental change

Special Issue Information

Dear Colleagues,

Recent advancements in genomics and metagenomics have significantly deepened our understanding of environmental microorganisms, which play a crucial role in ecosystem functioning and biogeochemical cycles. High-throughput sequencing technologies have transformed microbial community studies, enabling metagenomic analyses that uncover the genetic diversity and functional capabilities of these organisms directly from environmental samples. The advanced genomics and bioinformatics tools have also enhanced our ability to predict how microorganisms adapt to environmental changes like climate change and pollution. Overall, the convergence of genomics and ecology is reshaping our understanding of environmental microorganisms, highlighting their critical roles in maintaining ecological balance and addressing environmental challenges.

The aim of this Special Issue of Microorganisms is to collect innovative research and reviews that explore the genomic and ecological aspects of environmental microorganisms across diverse habitats, including marine, terrestrial, human, and built environments. We seek contributions that highlight the application of high-throughput sequencing and bioinformatics in uncovering microbial diversity and function, as well as their implications for ecosystem health and environmental sustainability.

Dr. Renxing Liang
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

  • genomics
  • environmental microorganisms
  • microbial communities
  • high-throughput sequencing
  • metagenome
  • bioinformatics
  • microbial ecology
  • biogeochemical cycles
  • biodegradation
  • bioremediation

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

19 pages, 2685 KiB  
Article
Thresholds and Trade-Offs: Fire Severity Modulates Soil Microbial Biomass-Function Coupling in Taiga Forests, Northeast of China
by Huijiao Qu, Siyu Jiang, Zhichao Cheng, Dan Wei, Libin Yang and Jia Zhou
Microorganisms 2025, 13(6), 1318; https://doi.org/10.3390/microorganisms13061318 - 5 Jun 2025
Abstract
Forest fires critically disrupt soil ecosystems by altering physicochemical properties and microbial structure-function dynamics. This study assessed short-term impacts of fire intensities (light/moderate/heavy) on microbial communities in Larix gmelinii forests one year post-fire. Using phospholipid fatty acid (PLFA) and Biolog EcoPlate analyses, we [...] Read more.
Forest fires critically disrupt soil ecosystems by altering physicochemical properties and microbial structure-function dynamics. This study assessed short-term impacts of fire intensities (light/moderate/heavy) on microbial communities in Larix gmelinii forests one year post-fire. Using phospholipid fatty acid (PLFA) and Biolog EcoPlate analyses, we found the following: (1) fire reduced soil organic carbon (SOC), dissolved organic carbon (DOC), total nitrogen (TN), and available nitrogen/potassium (AN/AK) via pyrolytic carbon release, while heavy-intensity fires enriched available phosphorus (AP), AN, and AK through ash deposition. (2) Thermal mortality and nutrient-pH-moisture stress persistently suppressed microbial biomass and metabolic activity. Moderate fires increased taxonomic richness but reduced functional diversity, confirming “functional redundancy.” (3) Neither soil microbial biomass nor metabolic activity at the fire site reached pre-fire levels after one year of recovery. Our findings advance post-fire soil restoration frameworks and advocate multi-omics integration to decode fire-adapted functional gene networks, guiding climate-resilient forest management. Full article
(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)
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20 pages, 2829 KiB  
Article
Actinobacteria Emerge as Novel Dominant Soil Bacterial Taxa in Long-Term Post-Fire Recovery of Taiga Forests
by Siyu Jiang, Huijiao Qu, Zhichao Cheng, Xiaoyu Fu, Libin Yang and Jia Zhou
Microorganisms 2025, 13(6), 1262; https://doi.org/10.3390/microorganisms13061262 - 29 May 2025
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Abstract
The long-term post-fire recovery phase is a critical stage for forest ecosystems to progress toward regeneration and mature succession. During this process, soil bacteria exhibit greater environmental adaptability, rapidly driving nutrient cycling and facilitating vegetation restoration. This study investigated the community structure and [...] Read more.
The long-term post-fire recovery phase is a critical stage for forest ecosystems to progress toward regeneration and mature succession. During this process, soil bacteria exhibit greater environmental adaptability, rapidly driving nutrient cycling and facilitating vegetation restoration. This study investigated the community structure and diversity of soil bacteria during long-term recovery after forest fires in the cold temperate zone, focusing on soils from the 2000 fires in Daxing’anling. Soil samples were classified into Low (L), Moderate (M), and High (H) fire damage intensity, with bacterial community composition and diversity analyzed using Illumina sequencing technology. After long-term fire recovery, the contents of soil organic carbon, black carbon, total nitrogen, alkaline nitrogen, available phosphorus, and available potassium were significantly higher elevated (p < 0.05), and water content was significantly lower, compared with that in the control check (CK) group. Soil urease, fluorescein diacetate, soil acid phosphatase, and soil dehydrogenase activities were significantly higher, and soil sucrase activity was significantly lower in H. There was a significant difference in the Alpha diversity index among the groups. Compared with CK, the Shannon index was significantly increased (p < 0.05) in L, while both Chao1 and Shannon indices were significantly decreased (p < 0.05) in M and significantly higher in H than CK. The results of the PCoA showed that there was a significant difference in the Beta diversity of the bacterial community among the groups (R2 = 0.60 p = 0.001). The dominant bacteria groups were Proteobacteria and Acidobacteriota, while Actinobacteria became the new dominant group during the long-term post-fire recovery. AP, WC, DOC, MBC, S-DHA, and S-SC were significantly and positively correlated with soil bacterial diversity (p < 0.05). The results of the co-occurrence network analysis showed that all groups were dominated by symbiotic relationships, with M having the highest network complexity and strongest competitive effects. This study found that the physicochemical properties of soils recovered over a long period of time after fire returned to or exceeded the unfired forest condition. The Actinobacteria phylum became a new dominant bacterial group, with stronger network complexity and competition, in the process of forest recovery after moderate fire. Full article
(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)
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