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Microorganisms
Special Issues
Microbial Life and Ecology in Extreme Environments
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Microbial Life and Ecology in Extreme Environments

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 5067

Special Issue Editor

Dr. Lara Vimercati

E-Mail Website
Guest Editor
Department of Ecology and Evolutionary Biology, University of Colorado, Campus Box 334, Boulder, CO 80309, USA
Interests: microbial ecology; microbial diversity; environmental microbiology; applied microbiology; microbial life in extreme environments

Special Issue Information

Dear Colleagues,

Microorganisms thriving in extreme environments demonstrate incredible resilience and diversity, adapting to conditions such as extreme heat, cold, acidity, or salinity that are inhospitable to most life forms. From the boiling temperatures of geothermal springs to the biting cold of the cryosphere, these microbes showcase the breadth of life's potential.

The aim of this Special Issue is to delve into the intricate adaptations of these microorganisms in extreme environments, exploring their ecological roles and the genomic insights that reveal their evolutionary history.

As Guest Editor of this Special Issue, we invite you to submit original research articles, review articles, and short communications related to the topic.

Dr. Lara Vimercati
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

  • extremophiles
  • genomics
  • microbial diversity
  • microbial adaptation
  • microbial ecology
  • evolutionary strategies
  • extreme environments
  • environmental microbiology

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Published Papers (4 papers)

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Research

23 pages, 3735 KiB  
Article
Taxonomic Diversity and Antimicrobial Potential of Thermophilic Bacteria from Two Extreme Algerian Hot Springs
by Marwa Aireche, Mohamed Merzoug, Amaria Ilhem Hammadi, Zohra Yasmine Zater, Keltoum Bendida, Chaimaa Naila Brakna, Meryem Berrazeg, Ahmed Yassine Aireche, Yasmine Saidi, Svetoslav Dimitrov Todorov, Dallel Arabet and Djamal Saidi
Microorganisms 2025, 13(6), 1425; https://doi.org/10.3390/microorganisms13061425 - 19 Jun 2025
Viewed by 465
Abstract
This study investigated thermophilic bacterial communities from two Algerian hot springs: Hammam Debagh (94–98 °C), recognized as the second hottest spring in the world, and Hammam Bouhadjar (61–72 °C), one of the hottest in northwest Algeria. Thirty isolates were obtained, able to grow [...] Read more.
This study investigated thermophilic bacterial communities from two Algerian hot springs: Hammam Debagh (94–98 °C), recognized as the second hottest spring in the world, and Hammam Bouhadjar (61–72 °C), one of the hottest in northwest Algeria. Thirty isolates were obtained, able to grow between 45 °C and 80 °C, tolerating pH 5.0–12.0 and NaCl concentrations up to 3%. Colonies displayed diverse morphologies, from circular and smooth to star-shaped and Saturn-like forms. All isolates were characterized as Gram-positive, catalase-positive rods or filamentous bacteria. Identification by MALDI-TOF, rep-PCR and 16S rRNA sequencing classified them mainly within Bacillus, Brevibacillus, Aneurinibacillus, Geobacillus, and Aeribacillus, with Geobacillus predominating. Rep-PCR provided higher resolution, revealing intra-species diversity overlooked by MALDI-TOF MS and 16S rRNA. A subset of six isolates, mainly Geobacillus spp., was selected based on phenotypic and genotypic diversity and tested for antimicrobial activity against thermophilic target isolates from the same hot spring environments. Strong inhibition zones (~24 mm) were observed, with Geobacillus thermoleovorans B8 displaying the highest activity. Optimization on Modified Nutrient Agar medium with Gelrite enhanced antimicrobial production and inhibition clarity. These findings highlight the ecological and biotechnological significance of thermophilic bacteria from Algerian geothermal ecosystems. While this study focused on microbial interactions within thermophilic communities, the promising inhibitory profiles reported here provide a foundation for future research targeting foodborne and antibiotic-resistant pathogens, as part of broader efforts in biopreservation and sustainable antimicrobial development. Full article
(This article belongs to the Special Issue Microbial Life and Ecology in Extreme Environments)
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22 pages, 4027 KiB  
Article
Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico)
by Antonio González-Sánchez, Luis Lozano-Aguirre, Guadalupe Jiménez-Flores, Mariana López-Sámano, Alejandro García-de Los Santos, Miguel A. Cevallos and Sylvie Le Borgne
Microorganisms 2025, 13(4), 809; https://doi.org/10.3390/microorganisms13040809 - 2 Apr 2025
Viewed by 618
Abstract
Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, [...] Read more.
Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the Cupriavidus gilardii species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between C. gilardii CCUG38401T, NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (ars, czc, cop 1, sil-cop 2, cup, mmf, and mer) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the czc system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where Cupriavidus strains can be retrieved. Full article
(This article belongs to the Special Issue Microbial Life and Ecology in Extreme Environments)
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31 pages, 3933 KiB  
Article
The Genetic Determinants of Extreme UV Radiation and Desiccation Tolerance in a Bacterium Recovered from the Stratosphere
by Adam J. Ellington, Tyler J. Schult, Christopher R. Reisch and Brent C. Christner
Microorganisms 2025, 13(4), 756; https://doi.org/10.3390/microorganisms13040756 - 27 Mar 2025
Cited by 1 | Viewed by 1768
Abstract
Microbes that survive transport to and in the stratosphere endure extremes of low temperature, atmospheric pressure, and relative humidity, as well as high fluxes in ultraviolet radiation (UVR). The high atmosphere thus provides an ideal environment to explore the genetic and physiological determinants [...] Read more.
Microbes that survive transport to and in the stratosphere endure extremes of low temperature, atmospheric pressure, and relative humidity, as well as high fluxes in ultraviolet radiation (UVR). The high atmosphere thus provides an ideal environment to explore the genetic and physiological determinants conveying high tolerance to desiccation and UVR. In this study, we examined Curtobacterium aetherium L6-1, an actinobacterium obtained from stratospheric aerosol sampling that displays high resistance to desiccation and UVR. We found that its phylogenetic relatives are resistant to desiccation, but only C. aetherium displayed a high tolerance to UVR. Comparative genome analysis and directed evolution experiments implicated genes encoding photolyase, DNA nucleases and helicases, and catalases as responsible for UVR resistance in C. aetherium. Differential gene expression analysis revealed the upregulation of DNA repair and stress response mechanisms when cells were exposed to UVR, while genes encoding sugar transporters, sugar metabolism enzymes, and antioxidants were induced upon desiccation. Based on changes in gene expression as a function of water content, C. aetherium can modulate its metabolism through transcriptional regulation at very low moisture levels (Xw < 0.25 g H2O per gram dry weight). Uncovering the genetic underpinnings of desiccation and UVR resistance in C. aetherium provides new insights into how bacterial DNA repair and antioxidant mechanisms function to exhibit traits at the extreme ends of phenotypic distributions. Full article
(This article belongs to the Special Issue Microbial Life and Ecology in Extreme Environments)
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16 pages, 3753 KiB  
Article
Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile
by Claudia Vilo, Francisca Fábrega, Víctor L. Campos and Benito Gómez-Silva
Microorganisms 2024, 12(11), 2238; https://doi.org/10.3390/microorganisms12112238 - 5 Nov 2024
Viewed by 1522
Abstract
The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water [...] Read more.
The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds’ sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite. Full article
(This article belongs to the Special Issue Microbial Life and Ecology in Extreme Environments)
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