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Microorganisms
Special Issues
Earth Systems: Shaped by Microbial Life
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Earth Systems: Shaped by Microbial Life

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 1351

Special Issue Editor

Dr. Panagiota Stathopoulou

E-Mail Website
Guest Editor
Department of Sustainable Agriculture, University of Patras, Agrinio, Greece
Interests: microbiome diversity; insect symbionts; fish pathogens; non-tuberculous mycobacteria; extremophiles
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The key component within the Earth system is a collection of four parts called “spheres”: the lithosphere, hydrosphere, biosphere, and atmosphere, which involve many interactive processes. The “spheres” interact to produce the environments we are familiar with. Microorganisms, the planet's oldest inhabitants, are the main drivers for global biogeochemical cycles and impact the properties of their environments in a two-way interaction, affecting the planet's habitability and resources available to human populations.

Microbial communities with respect to geographical scales and environmental changes have been studied intensively, focusing on the triad composed of taxonomic, phylogenetic, and functional diversity. Bacteria, archaea, and fungi can form unique networks and survive under diverse conditions, including extreme temperature, pressure, pH, salinity, or even anthropogenic pressure. Recently, the power of new technologies and approaches, in particular sequencing, revealed the untapped reservoir of genetic and metabolic microbial diversity and could lead to the discovery of novel biomolecules, pathways, and capabilities involved in developing new drugs, biotechnological processes, environmental remediation methods or understanding of the microbial mechanisms in response to climate change and acquisition of important knowledge to society.
The Special Issue entitled "Earth Systems: Shaped by Microbial Life" aims to present a collection of articles and reviews on research on the essential link between microbial diversity patterns and ecosystem functioning.

Excellent and innovative manuscripts can be focused on (but are not limited to):

  1. Microorganisms and the geographic limits of life.
  2. The anthropogenic effect on microbial communities.
  3. Bioprospecting in “spheres”.
  4. Metagenomic approaches to grasp the full extent of microbial diversity.

Reviews, original research, and communications will be welcome.

Dr. Panagiota Stathopoulou
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

  • microbial diversity
  • extreme habitats
  • novel microorganisms
  • bioprospecting
  • anthropogenic impact
  • dark matter

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Published Papers (2 papers)

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Research

16 pages, 3906 KiB  
Article
Diversity, Composition, and Ecological Function of Endophytic Fungal Communities Associated with Erigeron breviscapus in China
by Yi Zhao, Hui Wu, Fang Wang, Liangzhou Zhao, Weijun Gong and Haiyan Li
Microorganisms 2025, 13(5), 1080; https://doi.org/10.3390/microorganisms13051080 - 6 May 2025
Viewed by 156
Abstract
Endophytic fungi (EF) play crucial roles in accelerating the accumulation of medicinal components and regulating the survival and reproduction of medicinal plants. Erigeron breviscapus is a well-known traditional Chinese medicinal plant with effective therapeutic effects and a wide application, but little is known [...] Read more.
Endophytic fungi (EF) play crucial roles in accelerating the accumulation of medicinal components and regulating the survival and reproduction of medicinal plants. Erigeron breviscapus is a well-known traditional Chinese medicinal plant with effective therapeutic effects and a wide application, but little is known about the diversity, community structure, and ecological roles of EF in this plant. Here, the EF communities associated with different tissues of E. breviscapus at two seasons were studied by high-throughput sequencing methods. Furthermore, FUNGuild was performed to predict the ecological functions of the fungi. Didymella was found to be the most dominant genus across all four tissues, followed by Plectosphaerella, Filobasidium, Cystofilobasidium, and Cladosporium. Notably, the dominant and unique genera and biomarkers of four tissues were different. Interestingly, it was found that the roots had the highest fungal richness and diversity in summer. Moreover, both PCoA plots and PERMANOVA analyses indicated that the tissue and season were main factors contributing to the differences in the fungal communities of E. breviscapus. FUNGuild prediction revealed that pathotroph–saprotroph fungi and undefined taxa accounted for a high proportion in the EF of E. breviscapus. We also found some valuable endophytes that encouraged deeper investigation. These findings provide a theoretical reference for the further development and utilization of EF resources in E. breviscapus. Full article
(This article belongs to the Special Issue Earth Systems: Shaped by Microbial Life)
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16 pages, 1024 KiB  
Article
Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg
by Antonios Kioukis, Antonio Pedro Camargo, Pavlos Pavlidis, Ioannis Iliopoulos, Nikos C Kyrpides and Ilias Lagkouvardos
Microorganisms 2025, 13(3), 598; https://doi.org/10.3390/microorganisms13030598 - 5 Mar 2025
Viewed by 705
Abstract
The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is [...] Read more.
The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life. Full article
(This article belongs to the Special Issue Earth Systems: Shaped by Microbial Life)
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