Special Issue "Genetics 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: 28 February 2019

Special Issue Editors

Guest Editor
Prof. Dr. Rafael Montalvo-Rodríguez

Department of Biology, University of Puerto Rico, Box 9000 Mayagüez, PR 00681, USA
Website | E-Mail
Interests: microbiology; microbial physiology and genetics; taxonomy; microbial life in extreme environments; metagenomics
Guest Editor
Prof. Julie A. Maupin-Furlow

Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
Website | E-Mail
Phone: 352-392-4095
Interests: archaea, extremophiles, molecular evolution, bioenergetics, regulatory networks, proteolytic systems, cofactors

Special Issue Information

Dear Colleagues,

Halophilic microorganisms can be found in all domains of life and can thrive in environments with high salt content. They have been a subject of study for many years due to their interesting properties and physiology. An understanding of the genetics of halophilic microorganisms (from gene expression and regulation to genomics) will help to better understand the mechanisms of how life can occur at high salinity levels. This Special Issue is dedicated to the Genetics of Halophilic Microorganisms and their viruses. Colleagues are cordially invited to contribute original research papers or reviews to this Special Issue.

Prof. Rafael Montalvo-Rodríguez
Prof. Julie A. Maupin-Furlow
Guest Editors

Manuscript Submission Information

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Keywords

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

Published Papers (3 papers)

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Research

Open AccessArticle Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase
Received: 30 October 2018 / Revised: 6 December 2018 / Accepted: 13 December 2018 / Published: 20 December 2018
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Abstract
The obligately anaerobic haloalkaliphilic bacterium Alkalitalea saponilacus can use xylan as the sole carbon source and produce propionate as the main fermentation product. Using mixed carbon sources of 0.4% (w/v) sucrose and 0.1% (w/v) birch [...] Read more.
The obligately anaerobic haloalkaliphilic bacterium Alkalitalea saponilacus can use xylan as the sole carbon source and produce propionate as the main fermentation product. Using mixed carbon sources of 0.4% (w/v) sucrose and 0.1% (w/v) birch xylan, xylanase production from A. saponilacus was 3.2-fold greater than that of individual carbon sources of 0.5% (w/v) sucrose or 0.5% (w/v) birch xylan. The xylanse is halostable and exhibits optimal activity over a broad salt concentration (2–6% NaCl). Its activity increased approximately 1.16-fold by adding 0.2% (v/v) Tween 20. To understand the potential genetic mechanisms of xylan degradation and molecular adaptation to saline-alkali extremes, the complete genome sequence of A. saponilacus was performed with the pacBio single-molecule real-time (SMRT) and Illumina Misseq platforms. The genome contained one chromosome with a total size of 4,775,573 bps, and a G+C genomic content of 39.27%. Ten genes relating to the pathway for complete xylan degradation were systematically identified. Furthermore, various genes were predicted to be involved in isosmotic cytoplasm via the “compatible-solutes strategy” and cytoplasmic pH homeostasis though the “influx of hydrogen ions”. The halostable xylanase from A. saponilacus and its genomic sequence information provide some insight for potential applications in industry under double extreme conditions. Full article
(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)
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Open AccessArticle Molecular Factors of Hypochlorite Tolerance in the Hypersaline Archaeon Haloferax volcanii
Genes 2018, 9(11), 562; https://doi.org/10.3390/genes9110562
Received: 8 October 2018 / Revised: 7 November 2018 / Accepted: 13 November 2018 / Published: 20 November 2018
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Abstract
Halophilic archaea thrive in hypersaline conditions associated with desiccation, ultraviolet (UV) irradiation and redox active compounds, and thus are naturally tolerant to a variety of stresses. Here, we identified mutations that promote enhanced tolerance of halophilic archaea to redox-active compounds using Haloferax volcanii [...] Read more.
Halophilic archaea thrive in hypersaline conditions associated with desiccation, ultraviolet (UV) irradiation and redox active compounds, and thus are naturally tolerant to a variety of stresses. Here, we identified mutations that promote enhanced tolerance of halophilic archaea to redox-active compounds using Haloferax volcanii as a model organism. The strains were isolated from a library of random transposon mutants for growth on high doses of sodium hypochlorite (NaOCl), an agent that forms hypochlorous acid (HOCl) and other redox acid compounds common to aqueous environments of high concentrations of chloride. The transposon insertion site in each of twenty isolated clones was mapped using the following: (i) inverse nested two-step PCR (INT-PCR) and (ii) semi-random two-step PCR (ST-PCR). Genes that were found to be disrupted in hypertolerant strains were associated with lysine deacetylation, proteasomes, transporters, polyamine biosynthesis, electron transfer, and other cellular processes. Further analysis revealed a ΔpsmA1 (α1) markerless deletion strain that produces only the α2 and β proteins of 20S proteasomes was hypertolerant to hypochlorite stress compared with wild type, which produces α1, α2, and β proteins. The results of this study provide new insights into archaeal tolerance of redox active compounds such as hypochlorite. Full article
(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)
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Graphical abstract

Open AccessArticle Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1)
Genes 2018, 9(10), 493; https://doi.org/10.3390/genes9100493
Received: 11 September 2018 / Revised: 5 October 2018 / Accepted: 8 October 2018 / Published: 12 October 2018
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Abstract
The halophilic myohalovirus Halobacterium virus phiH (ΦH) was first described in 1982 and was isolated from a spontaneously lysed culture of Halobacterium salinarum strain R1. Until 1994, it was used extensively as a model to study the molecular genetics of haloarchaea, but only [...] Read more.
The halophilic myohalovirus Halobacterium virus phiH (ΦH) was first described in 1982 and was isolated from a spontaneously lysed culture of Halobacterium salinarum strain R1. Until 1994, it was used extensively as a model to study the molecular genetics of haloarchaea, but only parts of the viral genome were sequenced during this period. Using Sanger sequencing combined with high-coverage Illumina sequencing, the full genome sequence of the major variant (phiH1) of this halovirus has been determined. The dsDNA genome is 58,072 bp in length and carries 97 protein-coding genes. We have integrated this information with the previously described transcription mapping data. PhiH could be classified into Myoviridae Type1, Cluster 4 based on capsid assembly and structural proteins (VIRFAM). The closest relative was Natrialba virus phiCh1 (φCh1), which shared 63% nucleotide identity and displayed a high level of gene synteny. This close relationship was supported by phylogenetic tree reconstructions. The complete sequence of this historically important virus will allow its inclusion in studies of comparative genomics and virus diversity. Full article
(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1)    Tentative title: Applying genome-resolved metagenomics to de-convolute the halophilic microbiome

Authors: Uritskiy G, J. Taylor, and J. DiRuggiero

Tentative abstract: The rapidly expanding field of whole-genome metagenomics (WMG) now allows for genome-resolved analysis of microbiomes through extraction of metagenome-assembled genomes (MAGs). In this review, we will explore how WMGs impacts the analysis of halophilic communities, and the types of information that can be gleaned from the high resolution that it offers. We describe the breakthrough research that MAG extraction from WMG data permitted, including analysis of CRISPR array evolution, virus-host interactions, functional potential and salt adaptations of individual strains, and strain dispersal and selection across time and space. Deconvolution of halophilic communities at the WMG level has been difficult due to the high GC content and high intra-sample strain heterogeneity, which made both metagenomic assembly and binning a challenge. Additionally, the lack of reference environmental halophilic genomes in public databases made commonly used software ineffective at functionally annotating halophilic metagenomes and MAGs. However, the WMG field has rapidly expanded in the past decade, and the available tools have improved to a point where they are applicable to even the most complex microbiomes. With this in mind, many common WMG analysis methods that are already being applied to simpler communities can now be used to expand our understanding of halophilic communities. We will address the potential pitfalls and limitations of conventional WMG analysis being applied to halophilic communities, and propose experimental and analytical strategies to overcome them. Finally, we will speculate the potential applications of other next-generation sequencing technologies to halophilic communities. In particular, metatranscriptomics coupled with WMG show promise to uncover the metabolic activity of halophilic communities as well as individual strains, long read technologies such as Nanopore and PacBio technologies can aid in the assembly of highly similar microbial strains, and Hi-C can assist in the binning of highly heterogeneous closely-related strains.

 

2)    Tentative title: Global metabolic response of Haloferax mediterranei to the use of a single amino acids as nitrogen source

Authors: Esclapez, J.; Bautista, V.; Camacho,M; Pire, C.; Zafrilla, B.; Cortés,M; Bonete, M.J.

Tentative abstract: The halophilic archaeon Haloferax mediterranei is able to grow in defined media using different inorganic salts or single amino acids as sole nitrogen source. The transcriptome analysis in the presence of nitrate, ammonium or nitrogen starvation revealed the overexpression and repression of genes related to amino acid metabolism. Specifically, genes involved in amino acids catabolic pathways (such as isoleucine, leucine and aspartate) are overexpressed while genes related to amino acids biosynthesis are underexpressed in media with nitrate.

Taking these results into account, a second microarray has been carried out to compare the transcriptome of cultures grown with ammonium or single amino acid as nitrogen source. Four amino acids have been analysed; aspartate, glutamine, asparagine and glutamate.  The present work describes changes in H. mediterranei metabolism according to the nitrogen source used and in the gene expression related to nitrogen metabolism. 

 

3)    Tentative title: Temporal Analysis of Microbial Communities from the Crystallizer Ponds in Cabo Rojo Using Metagenomics

Authors: Ricardo Couto-Rodríguez* and Rafael Montalvo-Rodríguez

Tentative Abstract: The Cabo Rojo solar salterns is a hypersaline environment located at a tropical climate where conditions remain stable throughout the year allowing the establishment of steady microbial communities. The main goal of this study was to describe the microbial community in terms of structure and metabolic processes across time using metagenomics techniques. Three samplings (December 2014, March and July 2016) were carried out (50L each), where samples were filtered through a Millipore pressurized filtering system. DNA was subsequently extracted using physical-chemical methods and sequenced using paired end Illumina technologies. The sequencing effort produced 3 paired end libraries with a total of 111,816,040 reads that were subsequently assembled into 3 metagenomes. 12 distinct phyla were detected in our environmental samples. The microbial diversity was dominated in all three samples by the phylum Euryarchaeota, followed by Bacteroidetes and Proteobacteria. However, assessment at the genus level revealed a change in predominance across all three samples with Salinibacter predominating in the first sample whereas Halorubrum and Halogeometricum predominated in the second and third samples respectively. Anthropogenic impact as well as precipitation events may be contributing factors to the changes observed in the microbial community composition. Furthermore, functional annotation was carried out in order to detect genes related to ecological processes such as carbon, nitrogen and sulfur cycles. The presence of sequences related to microorganisms involved in nitrogen fixation, ammonia oxidation, sulfate reduction, sulfur oxidation and finally phosphate solubilizing were also detected. Using a metagenomic approach, a large diversity previously unreported in marine salterns at 34% NaCl(w/v) has been uncovered. When compared to other salterns around the world, the Cabo Rojo salterns offer a different community composition and a higher diversity. Moreover, analysis of gene composition highlights the importance of the microbial community in the biogeochemical cycles.

 

4)    Tentative title: Back to the salt mines: Genome and transcriptome analyses of the halophilic Hallstatt fungus Aspergillus salisburgensis

Authors: Tafer, H.; Poyntner C.; Pinar G.; Lopandic K.; Sterflinger-Gleixner K.

Tentative abstract: Salt mines are among the most extreme environment as they combine darkness, low nutrient availability and hypersaline conditions. We describe in this work the adaptive strategies of the true halophile Aspergillus salisburgensis found in a salt mine in Austria and compare them to the ex-type halotolerant strain Aspergillus sclerotialis. On a genomic level, Aspergillus salisburgensis exhibits a reduced genome size compared to Aspergillus sclerotialis as well as a contraction of genes involved in transport processes. The proteome of A. salisburgensis has an increased proportion of alanine, glycine and proline compared to the proteome of non-halophilic species. Transcriptome analyses of both strains growing at 5% and 20% NaCl show that A. salisburgensis regulates three times fewer genes than A. sclerotialis in order to adapt to the higher salt concentration. In A. sclerotialis, the increased osmotic stress impacted processes related to translation, transcription, transport and energy, while in the halophile strain membrane-related proteins were significantly affected.

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