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Microorganisms
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Microbial Evolution of Extremophiles
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Microbial Evolution of Extremophiles

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 15055

Special Issue Editors

Prof. Dr. Paul Blum

E-Mail Website
Guest Editor
School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, NE, USA
Interests: hyperthermophilic archaea; pathogenic enteric bacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Sophie Payne

E-Mail Website
Guest Editor
School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, NE, USA
Interests: hyperthermophilic archaea; pathogenic enteric bacteria

Special Issue Information

Dear Colleagues,

The study of microbial extremophiles has identified their diverse metabolic and physiological capabilities, culminating in incredible revelations regarding the features and limitations of biology. Furthermore, modern phylogenetics clusters extant extremophiles near the universal ancestor, emphasizing the importance in studying the evolutionary origin and subsequent diversification of life. The study of extremophile evolution has remarkable value in providing insight into past evolutionary history, modern mechanisms of extremophilicity, the manipulation of microbial evolution, and predictions in exobiology.

For this Special Issue of Microorganisms, we invite you to submit articles on the topic of evolution and relevant processes in microbial extremophiles. This includes topics such as the evolutionary history of life and its processes, mechanisms for evolution and adaptation, applications of evolutionary processes, and evolutionary predictions.

Prof. Dr. Paul Blum
Dr. Sophie Payne
Guest Editors

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

  • extremophile evolution
  • origin of life
  • phylogeny
  • bioinformatics
  • biotechnology
  • extremophile adaptation
  • evolutionary mechanisms
  • astrobiology
  • thermophiles
  • psychrophiles
  • acidophiles
  • alkaliphiles
  • osmophiles
  • halophiles
  • bacteria
  • archaea
  • eukaryotes

Published Papers (5 papers)

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Research

17 pages, 15059 KiB  
Article
Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan
by Herón Navarrete-Euan, Zuemy Rodríguez-Escamilla, Ernesto Pérez-Rueda, Karla Escalante-Herrera and Mario Alberto Martínez-Núñez
Microorganisms 2021, 9(4), 877; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040877 - 20 Apr 2021
Cited by 4 | Viewed by 3393
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal [...] Read more.
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity. Full article
(This article belongs to the Special Issue Microbial Evolution of Extremophiles)
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22 pages, 4467 KiB  
Article
The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances
by Phillip Seitzer, Andrew I. Yao, Ariana Cisneros and Marc T. Facciotti
Microorganisms 2020, 8(12), 1900; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8121900 - 30 Nov 2020
Cited by 1 | Viewed by 1837
Abstract
Operons are a dominant feature of bacterial and archaeal genome organization. Numerous investigations have related aspects of operon structure to operon function, making operons exemplars for studies aimed at deciphering Nature’s design principles for genomic organization at a local scale. We consider this [...] Read more.
Operons are a dominant feature of bacterial and archaeal genome organization. Numerous investigations have related aspects of operon structure to operon function, making operons exemplars for studies aimed at deciphering Nature’s design principles for genomic organization at a local scale. We consider this understanding to be both fundamentally important and ultimately useful in the de novo design of increasingly complex synthetic circuits. Here we analyze the evolution of the genomic context of operon-like structures in a set of 76 sequenced and annotated species of halophilic archaea. The phylogenetic depth and breadth of this dataset allows insight into changes in operon-like structures over shorter evolutionary time scales than have been studied in previous cross-species analysis of operon evolution. Our analysis, implemented in the updated software package JContextExplorer finds that operon-like context as measured by changes in structure frequently differs from a sequence divergence model of whole-species phylogeny and that changes seem to be dominated by the exploration of novel regulatory relationships. Full article
(This article belongs to the Special Issue Microbial Evolution of Extremophiles)
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12 pages, 1315 KiB  
Article
UV-A Irradiation Increases Scytonemin Biosynthesis in Cyanobacteria Inhabiting Halites at Salar Grande, Atacama Desert
by Gabriela Orellana, Benito Gómez-Silva, Milton Urrutia and Alexandra Galetović
Microorganisms 2020, 8(11), 1690; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111690 - 30 Oct 2020
Cited by 17 | Viewed by 2370
Abstract
Microbial consortia inhabiting evaporitic salt nodules at the Atacama Desert are dominated by unculturable cyanobacteria from the genus Halothece. Halite nodules provide transparency to photosynthetically active radiation and diminish photochemically damaging UV light. Atacama cyanobacteria synthesize scytonemin, a heterocyclic dimer, lipid soluble, [...] Read more.
Microbial consortia inhabiting evaporitic salt nodules at the Atacama Desert are dominated by unculturable cyanobacteria from the genus Halothece. Halite nodules provide transparency to photosynthetically active radiation and diminish photochemically damaging UV light. Atacama cyanobacteria synthesize scytonemin, a heterocyclic dimer, lipid soluble, UV-filtering pigment (in vivo absorption maximum at 370 nm) that accumulates at the extracellular sheath. Our goal was to demonstrate if UV-A irradiations modulate scytonemin biosynthesis in ground halites containing uncultured Halothece sp. cyanobacteria. Pulverized halite nodules with endolithic colonization were incubated under continuous UV-A radiation (3.6 W/m2) for 96 h, at 67% relative humidity, mimicking their natural habitat. Scytonemin content and relative transcription levels of scyB gene (a key gene in the biosynthesis of scytonemin) were evaluated by spectrophotometry and quantitative RT-PCR, respectively. After 48 h under these experimental conditions, the ratio scytonemin/chlorophyll a and the transcription of scyB gene increased to a maximal 1.7-fold value. Therefore, endolithic Halothece cyanobacteria in halites are metabolically active and UV radiation is an environmental stressor with a positive influence on scyB gene transcription and scytonemin biosynthesis. Endolithobiontic cyanobacteria in Atacama show a resilient evolutive and adaptive strategy to survive in one of the most extreme environments on Earth. Full article
(This article belongs to the Special Issue Microbial Evolution of Extremophiles)
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15 pages, 1624 KiB  
Article
Complete Genome of a Member of a New Bacterial Lineage in the Microgenomates Group Reveals an Unusual Nucleotide Composition Disparity Between Two Strands of DNA and Limited Metabolic Potential
by Vitaly V. Kadnikov, Andrey V. Mardanov, Alexey V. Beletsky, Olga V. Karnachuk and Nikolai V. Ravin
Microorganisms 2020, 8(3), 320; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8030320 - 25 Feb 2020
Cited by 8 | Viewed by 3413
Abstract
The candidate phyla radiation is a large monophyletic lineage comprising unculturable bacterial taxa with small cell and genome sizes, mostly known from genomes obtained from environmental sources without cultivation. Here, we present the closed complete genome of a member of the superphylum Microgenomates [...] Read more.
The candidate phyla radiation is a large monophyletic lineage comprising unculturable bacterial taxa with small cell and genome sizes, mostly known from genomes obtained from environmental sources without cultivation. Here, we present the closed complete genome of a member of the superphylum Microgenomates obtained from the metagenome of a deep subsurface thermal aquifer. Phylogenetic analysis indicates that the new bacterium, designated Ch65, represents a novel phylum-level lineage within the Microgenomates group, sibling to the candidate phylum Collierbacteria. The Ch65 genome has a highly unusual nucleotide composition with one strand of highly enriched in cytosine versus guanine throughout the whole length. Such nucleotide composition asymmetry, also detected in the members of Ca. Collierbacteria and Ca. Beckwithbacteria, suggests that most of the Ch65 chromosome is replicated in one direction. A genome analysis predicted that the Ch65 bacterium has fermentative metabolism and could produce acetate and lactate. It lacks respiratory capacity, as well as complete pathways for the biosynthesis of lipids, amino acids, and nucleotides. The Embden–Meyerhof glycolytic pathway and nonoxidative pentose phosphate pathway are mostly complete, although glucokinase, 6-phosphofructokinase, and transaldolase were not found. The Ch65 bacterium lacks secreted glycoside hydrolases and conventional transporters for importing sugars and amino acids. Overall, the metabolic predictions imply that Ch65 adopts the lifestyle of a symbiont/parasite, or a scavenger, obtaining resources from the lysed microbial biomass. We propose the provisional taxonomic assignment ‘Candidatus Chazhemtobacterium aquaticus’, genus ‘Chazhemtobacterium‘, family ‘Chazhemtobacteraceae‘ in the Microgenomates group. Full article
(This article belongs to the Special Issue Microbial Evolution of Extremophiles)
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18 pages, 9797 KiB  
Article
Janthinobacterium CG23_2: Comparative Genome Analysis Reveals Enhanced Environmental Sensing and Transcriptional Regulation for Adaptation to Life in an Antarctic Supraglacial Stream
by Markus Dieser, Heidi J. Smith, Thiruvarangan Ramaraj and Christine M. Foreman
Microorganisms 2019, 7(10), 454; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms7100454 - 15 Oct 2019
Cited by 5 | Viewed by 3470
Abstract
As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium [...] Read more.
As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements—functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment. Full article
(This article belongs to the Special Issue Microbial Evolution of Extremophiles)
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