Special Issue "Genetics of Halophilic Microorganisms"
Deadline for manuscript submissions: 28 February 2019
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
Manuscript Submission Information
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- Halophilic microorganisms
- Molecular Evolution
- Hypersaline habitats
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.