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Molecular Genetics and Genomics of Halophilic Microorganisms
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Molecular Genetics and Genomics of Halophilic Microorganisms

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 July 2020) | Viewed by 10868

Special Issue Editors

Prof. Dr. Rafael Montalvo-Rodríguez

E-Mail Website
Guest Editor
Department of Biology, University of Puerto Rico, Box 9000, Mayagüez, PR 00681, USA
Interests: microbiology; microbial physiology and genetics; taxonomy; microbial life in extreme environments; metagenomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Antonio Ventosa

E-Mail Website
Guest Editor
Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 4, 41004 Sevilla, Spain
Interests: halophiles; halophilic archaea; halophilic bacteria; hypersaline habitats; comparative genomics; phylogenomics; molecular systematics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Halophilic microorganisms normally thrive in environments with high salinity, and representatives can be found in all domains of life. The main goal of this Special Issue entitled “Molecular Genetics and Genomics of Halophilic Microorganisms” is to gather knowledge in the areas of genetics and physiology of halophilic microorganisms (from gene expression, regulation, metagenomics, to comparative genomics) and their viruses. This might be another step in understanding the mechanisms of how life can occur at high salinity. Colleagues are cordially invited to contribute original research papers or reviews to this Special Issue.

Prof. Dr. Rafael Montalvo-Rodríguez
Prof. Dr. Antonio Ventosa
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. Genes 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 2600 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

  • Halophilic microorganisms
  • Genetics
  • Genomics
  • Molecular Evolution
  • Hypersaline habitats
  • Extremophiles

Published Papers (3 papers)

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Research

12 pages, 1762 KiB  
Article
Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans
by Michael Sadler, Melanie R. Mormile and Ronald L. Frank
Genes 2020, 11(5), 484; https://doi.org/10.3390/genes11050484 - 29 Apr 2020
Cited by 4 | Viewed by 2618
Abstract
Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. [...] Read more.
Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Halophilic Microorganisms)
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15 pages, 3417 KiB  
Article
Comparative Genomics of Two New HF1-like Haloviruses
by Mike Dyall-Smith, Sen-Lin Tang, Brendan Russ, Pei-Wen Chiang and Friedhelm Pfeiffer
Genes 2020, 11(4), 405; https://doi.org/10.3390/genes11040405 - 08 Apr 2020
Cited by 9 | Viewed by 3212
Abstract
Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely [...] Read more.
Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely separated hypersaline lakes in Australia. Both are myoviruses with linear dsDNA genomes and infect the haloarchaeon Halorubrum coriense. Both genomes possess long, terminal direct repeat (TDR) sequences (320 bp for Serpecor1 and 306 bp for Hardycor2). The Serpecor1 genome is 74,196 bp in length, 57.0% G+C, and has 126 annotated coding sequences (CDS). Hardycor2 has a genome of 77,342 bp, 55.6% G+C, and 125 annotated CDS. They show high nucleotide sequence similarity to each other (78%) and with HF1 (>75%), and carry similar intergenic repeat (IR) sequences to those originally described in HF1 and HF2. Hardycor2 carries a DNA methyltransferase gene in the same genomic neighborhood as the methyltransferase genes of HF1, HF2 and HRTV-5, but is in the opposite orientation, and the inferred proteins are only distantly related. Comparative genomics allowed us to identify the candidate genes mediating cell attachment. The genomes of Serpecor1 and Hardycor2 encode numerous small proteins carrying one or more CxxC motifs, a signature feature of zinc-finger domain proteins that are known to participate in diverse biomolecular interactions. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Halophilic Microorganisms)
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24 pages, 4953 KiB  
Article
Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses
by Hugo Gildardo Castelán-Sánchez, Paola Elorrieta, Pedro Romoacca, Arturo Liñan-Torres, José Luis Sierra, Ingrid Vera, Ramón Alberto Batista-García, Silvia Tenorio-Salgado, Gabriel Lizama-Uc, Ernesto Pérez-Rueda, María Antonieta Quispe-Ricalde and Sonia Dávila-Ramos
Genes 2019, 10(11), 891; https://doi.org/10.3390/genes10110891 - 05 Nov 2019
Cited by 11 | Viewed by 4507
Abstract
Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was [...] Read more.
Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems. Full article
(This article belongs to the Special Issue Molecular Genetics and Genomics of Halophilic Microorganisms)
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