Advances in Microbial Adaptation and Evolution

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

Deadline for manuscript submissions: 30 November 2026 | Viewed by 1926

Editors


E-Mail Website
Guest Editor
Department of Biology, North Carolina Agricultural and Technical State University, 1601 E. Market Street, Greensboro, NC 27411, USA
Interests: microbial adaptation; bacterial resistance to antibiotics

E-Mail Website
Guest Editor
Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
Interests: microbial adaptation; bacterial resistance to antibiotics

Special Issue Information

Dear Colleagues,

Microorganisms inhabit dynamic and often hostile environments, and their ability to rapidly adapt is central to their ecological success, pathogenicity, and persistence under stress. Adaptation operates across multiple biological scales—from molecular sensing and regulatory rewiring to physiological trade-offs and evolutionary innovation—and is shaped by both environmental pressures and genetic constraints. Understanding these adaptive trajectories is critical for predicting microbial behavior in clinical, industrial, and natural ecosystems.

This Special Issue highlights current advances in microbial adaptation by integrating mechanistic, ecological, and evolutionary perspectives. We welcome studies that probe how selective pressures shape genetic and regulatory architectures; how stress responses transition into heritable evolutionary change; and how pleiotropy, epistasis, and environmental complexity drive or constrain adaptive outcomes. Key questions include: When is adaptation predictable versus contingent? How do regulatory networks facilitate evolvability? What costs accompany adaptive gains? And how do long-term dynamics differ from short-term acclimation?

We invite submissions that explore microbial adaptation through experimental evolution, genomics, transcriptomics, systems biology, and high-resolution phenotyping. Topics of interest include regulatory adaptation, antimicrobial and metal stress evolution, niche specialization, cross-protection and trade-offs, host-microbe evolutionary dynamics, and adaptation to physicochemical surfaces or microenvironments. Both original research and synthetic perspectives are encouraged, particularly those linking mechanistic insight with evolutionary consequence.

Dr. Misty D. Thomas
Prof. Dr. Joseph L. Graves Jr.
Guest Editors

Manuscript Submission Information

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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 adaptation
  • experimental evolution
  • regulatory networks
  • two-component systems
  • stress response
  • pleiotropy
  • epistasis
  • antimicrobial resistance
  • genomic evolution
  • phenotype-environment interactions

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Published Papers (3 papers)

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Research

15 pages, 1854 KB  
Article
Rapid Evolution of Ionic Silver Resistance in Escherichia Phage T7
by Larisa Chila Kiki, Monela Ntonifor, Walter LaDelle, Ugonna Morikwe, Franklin Ezeanowai, Lindsey McGee, Akamu Ewunkem, Joseph Graves, Jr. and Liesl Jeffers-Francis
Microorganisms 2026, 14(6), 1243; https://doi.org/10.3390/microorganisms14061243 - 1 Jun 2026
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Abstract
The antimicrobial resistance crisis has led to the use of metals and bacteriophages as possible alternatives to antibiotics. Experimental studies have examined interactions between ionic/nano-silver and bacteriophages against multidrug-resistant bacteria. However, these approaches have often failed to examine whether silver affects the stability [...] Read more.
The antimicrobial resistance crisis has led to the use of metals and bacteriophages as possible alternatives to antibiotics. Experimental studies have examined interactions between ionic/nano-silver and bacteriophages against multidrug-resistant bacteria. However, these approaches have often failed to examine whether silver affects the stability and infectivity of bacteriophages. Here, we utilized experimental evolution to evolve resistance to ionic silver in bacteriophage T7. High ionic silver concentrations that do not represent physiological exposure conditions were used to impose strong selective pressure. Evolution of ionic silver resistance in phage T7 was rapid, as evidenced by recovery of bacteriophage growth in E. coli following repeated exposures to ionic silver, enhanced infectivity of silver-selected populations relative to parallel control and ancestral populations under increasing ionic silver concentrations, and greater suppression of E. coli growth in standard medium. Furthermore, silver resistance evolved without loss of thermal or pH stability under the conditions tested. The genomic foundation of silver resistance was relatively simple, with positive and negative natural selection differentiating the silver-selected populations from the controls and ancestral populations across serial passages in silver. Support for replication-associated adaptation under ionic silver selection may be reflected in recurrent mutations identified in genes involved in transcription, DNA replication, and genome maintenance, including T7p07 (RNA polymerase), T7p10 (DNA ligase), and T7p29 (DNA polymerase I). These findings highlight the importance of evaluating phage –silver combination strategies within an evolutionary framework that accounts for the adaptive capacity of bacteriophages under silver selection. Full article
(This article belongs to the Special Issue Advances in Microbial Adaptation and Evolution)
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22 pages, 3403 KB  
Article
Green-Synthesized vs. Chemical Silver Nanoparticles: A Comparative Study on S. aureus Adaptability and Cross-Activity
by Akamu Ewunkem, Josiah Dixon, Jordan Queenie, Uchenna Iloghalu, Franklin Ezeanowai and Sada Boyd
Microorganisms 2026, 14(5), 1114; https://doi.org/10.3390/microorganisms14051114 - 14 May 2026
Viewed by 454
Abstract
Rising antibiotic resistance necessitates alternatives such as silver nanoparticles (AgNPs), which exhibit bactericidal activity via multi-target mechanisms (e.g., membrane disruption, ROS production). While resistance to chemically synthesized AgNPs exists, the potential for resistance to green-synthesized AgNPs, such as those from reishi mushroom, is [...] Read more.
Rising antibiotic resistance necessitates alternatives such as silver nanoparticles (AgNPs), which exhibit bactericidal activity via multi-target mechanisms (e.g., membrane disruption, ROS production). While resistance to chemically synthesized AgNPs exists, the potential for resistance to green-synthesized AgNPs, such as those from reishi mushroom, is unknown. This study compared S. aureus resistance development against both AgNP types using experimental evolution by analyzing genomic and morphological changes. Additionally, this work evaluated potential cross-resistance responses to ionic silver and investigated how adaptation to green-synthesized AgNPs affects sensitivity to chemically synthesized AgNPs (and vice versa). Rapid resistance, along with cross-resistance to silver ions, emerged in bacteria following 14 days of sublethal exposure to silver nanoparticles, regardless of whether they were chemically or biologically synthesized. While green-synthesized AgNPs demonstrated a substantial resistance to chemical variants (p < 0.05), the reverse effect was not as strong, and resistant populations showed distinct morphological adaptations. Genomic analysis highlighted convergent hard selective sweeps, identifying common mutations across both chemical and green AgNP-treated populations, with limited unique mutations found for either. These findings enhance our understanding of bacterial resistance mechanisms to nanomaterials, contributing to the development of safer, eco-friendly, and high-efficacy treatments against multidrug-resistant infection. Full article
(This article belongs to the Special Issue Advances in Microbial Adaptation and Evolution)
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15 pages, 1674 KB  
Article
Transcriptomic Analysis of Fusarium verticillioides Across Different Cultivation Periods Reveals Dynamic Gene Expression Changes
by Meng-Ling Deng, Jun-Jun He, Xin-Yan Xie, Jian-Fa Yang, Fan-Fan Shu, Feng-Cai Zou, Lu-Yang Wang and Jun Ma
Microorganisms 2026, 14(1), 102; https://doi.org/10.3390/microorganisms14010102 - 2 Jan 2026
Viewed by 702
Abstract
Fusarium verticillioides is a common pathogenic fungus of corn since it causes severe yield losses and produces mycotoxins to threaten the health of both humans and livestock. Although extensive research has characterized specific genetic and environmental factors influencing mycotoxin production, a systematic understanding [...] Read more.
Fusarium verticillioides is a common pathogenic fungus of corn since it causes severe yield losses and produces mycotoxins to threaten the health of both humans and livestock. Although extensive research has characterized specific genetic and environmental factors influencing mycotoxin production, a systematic understanding of the temporal transcriptional dynamics governing its developmental progression remains lacking. This study addresses this critical knowledge gap through a time-series transcriptomic analysis of F. verticillioides at four key cultivation stages (3, 5, 7, and 9 days post-inoculation). Transcriptomic analysis identified 1928, 2818, and 1934 differentially expressed genes (DEGs) in the comparisons of FV3 vs. FV5, FV5 vs. FV7, and FV7 vs. FV9, respectively. Gene Ontology enrichment revealed 76, 106, and 56 significantly enriched terms across these comparisons, with “integral component of membrane” consistently being the most enriched cellular component. Pathway analysis demonstrated “amino acid metabolism” and “carbohydrate metabolism” as the most significantly enriched metabolic pathways. Notably, the fumonisin (FUM) and fusaric acid (FA) biosynthetic gene clusters exhibited coordinated peak expression during the early cultivation, followed by progressive decline. Mfuzz clustering further delineated 12 distinct expression trajectories, highlighting the dynamic transcriptional networks underlying fungal adaptation. This work provided the first comprehensive temporal transcriptome of F. verticillioides, establishing a foundational resource for understanding its stage-specific biology and revealing potential time-sensitive targets for future intervention strategies. Full article
(This article belongs to the Special Issue Advances in Microbial Adaptation and Evolution)
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