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Microorganisms
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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 1783

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 (4 papers)

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Research

13 pages, 968 KiB  
Article
Identification of Parasitic Infections by Analyzing Honeybees, Honey, and Pollen Using Droplet Digital RT-PCR
by Luigi Jacopo D’Auria, Andrea Mancusi, Yolande Thérèse Rose Proroga, Irene Dini, Tiziana Cardellicchio, Orlandina Di Maro, Sabato De Vita, Marica Egidio, Raffaele Marrone and Giuseppe Rofrano
Microorganisms 2025, 13(7), 1487; https://doi.org/10.3390/microorganisms13071487 - 26 Jun 2025
Viewed by 50
Abstract
Toxoplasma gondii, Giardia intestinalis, and Cryptosporidium spp. are common pathogens that contaminate water and food. They can pose serious health risks, especially to vulnerable groups like immunocompromised individuals, pregnant women, young children, and aging people. An all-encompassing approach to minimizing transmission [...] Read more.
Toxoplasma gondii, Giardia intestinalis, and Cryptosporidium spp. are common pathogens that contaminate water and food. They can pose serious health risks, especially to vulnerable groups like immunocompromised individuals, pregnant women, young children, and aging people. An all-encompassing approach to minimizing transmission involves identifying effective techniques for detecting, treating, and preventing protozoan parasites. This study confirmed the effectiveness of a Droplet Digital Reverse Transcription Polymerase Chain Reaction (dd RT-PCR) method for quickly and accurately identifying Toxoplasma gondii, Giardia intestinalis, and Cryptosporidium species in honeybees, honey, and pollen by using ISO 17468 and ISO 16140 standard guidelines. The study evaluated honeybee (n = 16), honey (n = 12), and pollen (n = 8) samples collected from various apiaries in Southern Italy between June and September 2023. The results showed that honeybees, honey, and pollen can be considered bioindicators of infections by T. gondii, G. intestinalis, and Cryptosporidium spp. Furthermore, pollen, along with honey to a lesser degree, can serve as significant indicators for evaluating food safety. Therefore, it is essential to monitor their quality and purity due to environmental influences. Full article
(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)
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16 pages, 9902 KiB  
Article
Genome Sequences of the First Phages Infecting Limnohabitans Reveal Their Global Distribution and Metabolic Potential
by Boxuan Deng, Raoqiong Che, Pinxin Zhu, Yongxia Wang, Zhiying Li, Shiying Zhang and Wei Xiao
Microorganisms 2025, 13(6), 1324; https://doi.org/10.3390/microorganisms13061324 - 6 Jun 2025
Viewed by 392
Abstract
Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety [...] Read more.
Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. Limnohabitans, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting Limnohabitans have been reported to date. Here, we describe, for the first time, three phages infecting Limnohabitans, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on Limnohabitans in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding Limnohabitans–phage interactions. Full article
(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)
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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
Viewed by 446
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
Viewed by 329
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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