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Microorganisms
Special Issues
Exploring Microbial Evolution: From Cellular Dynamics to Phylogenetic Branching
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Exploring Microbial Evolution: From Cellular Dynamics to Phylogenetic Branching

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 717

Special Issue Editor

Prof. Dr. Nobuyuki Haga

E-Mail Website
Guest Editor
Department of Biological Sciences, Faculty of Science and Technology, Senshu University of Ishinomaki, Miyagi 986-8580, Japan
Interests: cell biology; mating-type substances in paramecium; mating reaction; clonal aging and rejuvenescence
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleague,

Recent advancements in analytical chemistry for DNA and other nucleic acids allow for extracting information regarding microorganisms from ancient soils and fossil remains. Another positive development is the progress in microbial culture technology, which provides opportunities to investigate existing organisms' life cycles and physiological functions.

This Special Issue will highlight cutting-edge research on microorganisms' evolutionary status in cellular physiology, biochemistry, molecular biology, and ecology and provide an opportunity to gain a comprehensive overview of these traits. We encourage research findings on organisms with novel and unexplored characteristics, particularly those emphasizing advancements in analytical chemistry about DNA and other nucleic acids and innovations in microbial culture technology. Submitted papers should relate to at least one of the following areas: cell physiology, cultivation, energy metabolism, genetic/genomic analysis, natural selection, phylogenetic trees, sexual/asexual reproduction, species identification, and symbiosis/parasitism; however, other areas are also acceptable.

This Special Issue gathers insights from researchers addressing the complex challenges related to the evolution of microorganisms. As Guest Editors of this Special Issue, we invite you to submit research articles, review articles, and short communications related to this topic.

Prof. Dr. Nobuyuki Haga
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

  • cell physiology
  • cultivation
  • energy metabolism
  • gene/genome analysis
  • natural selection
  • phylogenetic trees
  • sexual/asexual reproduction
  • species identification
  • and symbiosis/parasitism

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Published Papers (1 paper)

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Review

18 pages, 1398 KiB  
Review
Protists with Uncertain Phylogenetic Affiliations for Resolving the Deep Tree of Eukaryotes
by Euki Yazaki, Takashi Shiratori and Yuji Inagaki
Microorganisms 2025, 13(8), 1926; https://doi.org/10.3390/microorganisms13081926 - 18 Aug 2025
Viewed by 338
Abstract
Resolving the eukaryotic tree of life (eToL) remains a fundamental challenge in biology. Much of eukaryotic phylogenetic diversity is occupied by unicellular microbial eukaryotes (i.e., protists). Among these, the phylogenetic positions of a significant number of lineages remain unresolved due to limited data [...] Read more.
Resolving the eukaryotic tree of life (eToL) remains a fundamental challenge in biology. Much of eukaryotic phylogenetic diversity is occupied by unicellular microbial eukaryotes (i.e., protists). Among these, the phylogenetic positions of a significant number of lineages remain unresolved due to limited data and ambiguous traits. To address this issue, we introduce the term “PUPAs” (protists with uncertain phylogenetic affiliations) to collectively describe these lineages, instead of using vague or inconsistent labels, such as incertae sedis or orphan taxa. Historically, protists were classified based solely on morphological features, and many with divergent cell structures were left unplaced in the eToL. With the advent of sequence-based approaches, the phylogenetic affiliations of some PUPAs have been clarified using molecular markers, such as small subunit ribosomal DNA. The combination of technological progress and continuous efforts to cultivate diverse protists, including PUPAs and novel protists, now enables phylogenetic analyses based on hundreds of proteins, providing their concrete placements in the eToL. For example, these advances have led to the discovery of new deep-branching lineages (e.g., Hemimastigophora), the resolution of relationships among major groups (e.g., Microheliella, which linked Cryptista and Archaeplastida), and insights into evolutionary innovations within specific clades (e.g., Glissandra). In this review, we summarize current consensus in eukaryotic phylogeny and highlight recent findings on PUPAs whose phylogenetic affiliations have been clarified. We also discuss a few lineages for which the phylogenetic homes remain unsettled, the evolutionary implications of these discoveries, and the remaining challenges in resolving the complete eToL. Full article
(This article belongs to the Special Issue Exploring Microbial Evolution: From Cellular Dynamics to Phylogenetic Branching)
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