Genomics of Extremophiles and Archaea

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

Deadline for manuscript submissions: closed (15 February 2024) | Viewed by 12541

Special Issue Editors


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Guest Editor
Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
Interests: extremophiles; haloarchaea; microbial genomics; purple membrane; gas vesicle nanoparticles; vaccines and therapeutics
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Guest Editor
Institut Pasteur, Université Paris Cité, Département de biologie computationnelle, F-75015 Paris, France
Interests: metagenomics; HTS technologies; microbiology; bioinformatics

Special Issue Information

Dear Colleagues,

The number of sequenced extremophiles and archaea has significantly increased over the decades, driven by increasingly powerful sequencing and analysis methods. The resulting millions of genes and predicted proteins provide a potent resource for the advancement of both science and technology. Advanced technologies and bioinformatics are providing insights into methylation patterns, epigenetic characteristics and regulatory networks. The rich biology of these organisms has revealed mechanisms of tolerance and adaptation to extremes, as well as clues to the origin and evolution of life on Earth. Ground breaking research, including biochemical and genetic studies, physiological, structural, and synthetic biology approaches is defining the limits to life on Earth and shaping the search for life on Mars and elsewhere in the universe.

This Special Issue on extremophiles and archaea aims to spotlight studies that incorporate a combination of genomic, metagenomic, post-genomic, bioinformatic and experimental analyses. Reports on genomes from recently isolated novel species, including their analysis and utilization, are especially encouraged, as they provide insights into extreme environments, and biotechnological and/or biomedical applications.

As the Guest Editors of the Special Issue, it is our pleasure to invite you to submit your cutting-edge, interdisciplinary research articles and reviews related to extremophilic and archaeal genomics.

Prof. Dr. Shiladitya DasSarma
Dr. Sean P. Kennedy
Guest Editors

Manuscript Submission Information

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Keywords

  • sequencing
  • bioinformatics
  • methylation
  • microbial diversity
  • astrobiology
  • evolution
  • metagenomics

Published Papers (7 papers)

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Research

27 pages, 46413 KiB  
Article
Characterize the Growth and Metabolism of Acidithiobacillus ferrooxidans under Electroautotrophic and Chemoautotrophic Conditions
by Quansheng Wang, Haijun Long, Huiqi Wang and Maggie C. Y. Lau Vetter
Microorganisms 2024, 12(3), 590; https://doi.org/10.3390/microorganisms12030590 - 15 Mar 2024
Viewed by 681
Abstract
Acidophiles are capable of surviving in extreme environments with low pH. Acidithiobacillus ferrooxidans is a typical acidophilic bacterium that has been extensively studied when grown chemoautotrophically, i.e., when it derives energy from oxidation of Fe2+ or reduced inorganic sulfur compounds (RISCs). Although [...] Read more.
Acidophiles are capable of surviving in extreme environments with low pH. Acidithiobacillus ferrooxidans is a typical acidophilic bacterium that has been extensively studied when grown chemoautotrophically, i.e., when it derives energy from oxidation of Fe2+ or reduced inorganic sulfur compounds (RISCs). Although it is also known to grow with electrons supplied by solid electrodes serving as the sole source of energy, the understanding of its electroautotrophic growth is still limited. This study aimed to compare the growth characteristics of A. ferrooxidans under electroautotrophic (ea) and chemoautotrophic (ca) conditions, with an attempt to elucidate the possible mechanism(s) of extracellular electron flow into the cells. Jarosite was identified by Raman spectroscopy, and it accumulated when A. ferrooxidans used Fe2+ as the electron donor, but negligible mineral deposition occurred during electroautotrophic growth. Scanning electron microscopy (SEM) showed that A. ferrooxidans possesses more pili and extracellular polymeric substances (EPSs) under electroautotrophic conditions. A total of 493 differentially expressed genes (DEGs) were identified, with 297 genes being down-regulated and 196 genes being up-regulated in ea versus ca conditions. The genes known to be essential for chemoautotrophic growth showed a decreased expression in the electroautotrophic condition; meanwhile, there was an increased expression of genes related to direct electron transfer across the cell’s outer/inner membranes and transmembrane proteins such as pilin and porin. Joint analysis of DEGs and differentially expressed metabolites (DEMs) showed that galactose metabolism is enhanced during electroautotrophic growth, inducing A. ferrooxidans to produce more EPSs, which aids the cells in adhering to the solid electrode during their growth. These results suggested that electroautotrophy and chemoautotrophy of A. ferrooxidans have different extracellular electron uptake (EEU) pathways, and a model of EEU during electroautotrophic growth is proposed. The use of extracellular electrons as the sole energy source triggers A. ferrooxidans to adopt metabolic and subsequently phenotypic modifications. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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16 pages, 1298 KiB  
Article
A Survey of Archaeal Restriction–Modification Systems
by Brian P. Anton and Richard J. Roberts
Microorganisms 2023, 11(10), 2424; https://doi.org/10.3390/microorganisms11102424 - 28 Sep 2023
Viewed by 837
Abstract
When compared with bacteria, relatively little is known about the restriction–modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known [...] Read more.
When compared with bacteria, relatively little is known about the restriction–modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m6A and m4C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of “persistent” DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest “persistent” MTase groups, revealing that methylation of C(m5C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m6A, m4C, and m5C DNA MTases, respectively, occur in approximately the ratio 4:2:1. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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18 pages, 3212 KiB  
Article
The Genome of Varunaivibrio sulfuroxidans Strain TC8T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea
by Sushmita Patwardhan, Jonathan Phan, Francesco Smedile and Costantino Vetriani
Microorganisms 2023, 11(6), 1366; https://doi.org/10.3390/microorganisms11061366 - 23 May 2023
Cited by 1 | Viewed by 1067
Abstract
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its [...] Read more.
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin–Benson–Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism’s metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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18 pages, 1500 KiB  
Article
Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities
by José Q. García-Maldonado, Hever Latisnere-Barragán, Alejandra Escobar-Zepeda, Santiago Cadena, Patricia J. Ramírez-Arenas, Ricardo Vázquez-Juárez, Maurilia Rojas-Contreras and Alejandro López-Cortés
Microorganisms 2023, 11(3), 812; https://doi.org/10.3390/microorganisms11030812 - 22 Mar 2023
Cited by 3 | Viewed by 2167
Abstract
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic [...] Read more.
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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12 pages, 1866 KiB  
Communication
Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation
by Sicong Li, Jiahua Wang, Jie Liu, Hongcai Zhang, Tianqiang Bao, Chengwen Sun, Jiasong Fang and Junwei Cao
Microorganisms 2023, 11(3), 798; https://doi.org/10.3390/microorganisms11030798 - 21 Mar 2023
Cited by 1 | Viewed by 1725
Abstract
Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the [...] Read more.
Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the Mariana Trench at a depth of 5900 m. Here, we report its complete genome sequence and adaptation strategies for survival in deep-sea environments. MTB7 contains what is currently the third-largest genome among all isolated Shewanella strains and shows higher coding density than neighboring strains. Metabolically, MTB7 is predicted to utilize various carbon and nitrogen sources. D-amino acid utilization and HGT-derived purine-degrading genes could contribute to its oligotrophic adaptation. For respiration, the cytochrome o ubiquinol oxidase genes cyoABCDE, typically expressed at high oxygen concentrations, are missing. Conversely, a series of anaerobic respiratory genes are employed, including fumarate reductase, polysulfide reductase, trimethylamine-N-oxide reductase, crotonobetaine reductase, and Mtr subunits. The glycine reductase genes and the triplication of dimethyl sulfoxide reductase genes absent in neighboring strains could also help MTB7 survive in low-oxygen environments. Many genes encoding cold-shock proteins, glycine betaine transporters and biosynthetic enzymes, and reactive oxygen species-scavenging proteins could contribute to its low-temperature adaptation. The genomic analysis of MTB7 will deepen our understanding of microbial adaptation strategies in deep-sea environments. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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17 pages, 5859 KiB  
Article
Genomic Analysis of Haloarchaea from Diverse Environments, including Permian Halite, Reveals Diversity of Ultraviolet Radiation Survival and DNA Photolyase Gene Variants
by Sagorika Nag, Priya DasSarma, David J. Crowley, Rafael Hamawi, Samantha Tepper, Brian P. Anton, Daniel Guzmán and Shiladitya DasSarma
Microorganisms 2023, 11(3), 607; https://doi.org/10.3390/microorganisms11030607 - 28 Feb 2023
Viewed by 2668
Abstract
Ultraviolet (UV) radiation responses of extremophilic and archaeal microorganisms are of interest from evolutionary, physiological, and astrobiological perspectives. Previous studies determined that the halophilic archaeon, Halobacterium sp. NRC-1, which survives in multiple extremes, is highly tolerant of UV radiation. Here, Halobacterium sp. NRC-1 [...] Read more.
Ultraviolet (UV) radiation responses of extremophilic and archaeal microorganisms are of interest from evolutionary, physiological, and astrobiological perspectives. Previous studies determined that the halophilic archaeon, Halobacterium sp. NRC-1, which survives in multiple extremes, is highly tolerant of UV radiation. Here, Halobacterium sp. NRC-1 UV tolerance was compared to taxonomically diverse Haloarchaea isolated from high-elevation salt flats, surface warm and cold hypersaline lakes, and subsurface Permian halite deposits. Haloterrigena/Natrinema spp. from subsurface halite deposits were the least tolerant after exposure to photoreactivating light. This finding was attributed to deviation of amino acid residues in key positions in the DNA photolyase enzyme or to the complete absence of the photolyase gene. Several Halobacterium, Halorubrum and Salarchaeum species from surface environments exposed to high solar irradiance were found to be the most UV tolerant, and Halorubrum lacusprofundi from lake sediment was of intermediate character. These results indicate that high UV tolerance is not a uniform character trait of Haloarchaea and is likely reflective of UV exposure experienced in their environment. This is the first report correlating natural UV tolerance to photolyase gene functionality among Haloarchaea and provides insights into their survival in ancient halite deposits and potentially on the surface of Mars. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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27 pages, 2870 KiB  
Article
Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59T and Sphingomonas glaciei S8-45T, Two Novel Bacteria from the North Slope of Mount Everest
by Yang Liu, Xiaowen Cui, Ruiqi Yang, Yiyang Zhang, Yeteng Xu, Guangxiu Liu, Binglin Zhang, Jinxiu Wang, Xinyue Wang, Wei Zhang, Tuo Chen and Gaosen Zhang
Microorganisms 2022, 10(10), 2037; https://doi.org/10.3390/microorganisms10102037 - 14 Oct 2022
Cited by 1 | Viewed by 1932
Abstract
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m [...] Read more.
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59T and S8-45T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59T and S8-45T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59T and S8-45T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59T and S8-45T strains. Additionally, strain S5-59T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59T (=JCM 35564T =GDMCC 1.3193T) and S8-45T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59T and S8-45T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs. Full article
(This article belongs to the Special Issue Genomics of Extremophiles and Archaea)
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