Special Issue "Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016"

A special issue of Life (ISSN 2075-1729).

Deadline for manuscript submissions: closed (30 September 2016)

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. Dr. Aharon Oren

Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
Website | E-Mail
Phone: 972-2-6584951
Interests: Microbial life in extreme environments; Halophiles; Prokaryote; taxonomy and nomenclature
Guest Editor
Prof. Dr. Antonio Ventosa

Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
Website | E-Mail
Phone: +34-954556765
Fax: +34-954628162
Interests: halophiles; halophilic archaea; halophilic bacteria; hypersaline habitats; comparative genomics; phylogenomics; molecular systematics

Special Issue Information

Dear Colleagues,

Halophilic microorganisms have been a subject of study for many years due to their interesting genetics and physiology. On behalf of the International and Local Organizing Committees it is with great pleasure that we invite you to the 11th Conference on Halophilic Microorganisms “Halophiles 2016” (http://www.halophiles2016.org/). The meeting will be held in San Juan, Puerto Rico from 22 May to 27 May 2016. We hope you will be enriched by the scientific contributions and also enjoy the wonderful people, history, and the tropical environment that the Island of Puerto Rico has to offer.

The meeting will have different sessions in which invited speakers will discuss different aspects and recent findings of halophiles, such as Archaea, Bacteria, Eukarya and viruses. Sessions will cover topics on Taxonomy, Phylogeny and Biodiversity, Ecology, Physiology, Molecular Biology, Biochemistry, Genetics, Genomics, and Biotechnology. We encourage you to submit abstracts for poster presentation. Additionally, there will be a joint meeting of the ICSP-Subcommittees on the taxonomy of the Halobacteriaceae and Halomonadaceae.

I am delighted to welcome you to Puerto Rico! I really hope to see you in May 2016.

Participants in the conference are cordially invited to contribute original research papers or reviews to this Special Issue of Life.

Prof. Dr. Rafael Montalvo-Rodríguez
Prof. Dr. Aharon Oren
Prof. Dr. Antonio Ventosa
Guest Editors

Conference

Manuscript Submission Information

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Published Papers (8 papers)

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Editorial

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Open AccessEditorial Hans Georg Trüper (1936–2016) and His Contributions to Halophile Research
Received: 28 April 2016 / Revised: 6 May 2016 / Accepted: 6 May 2016 / Published: 12 May 2016
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Abstract
Prof. Hans Georg Trüper, one of the most important scientists in the field of halophile research, passed away on 9 March 2016 at the age of 79. I here present a brief obituary with special emphasis on Prof. Trüper’s contributions to our understanding [...] Read more.
Prof. Hans Georg Trüper, one of the most important scientists in the field of halophile research, passed away on 9 March 2016 at the age of 79. I here present a brief obituary with special emphasis on Prof. Trüper’s contributions to our understanding of the halophilic prokaryotes and their adaptations to life in hypersaline environments. He has pioneered the study of the halophilic anoxygenic phototrophic sulfur bacteria of the EctothiorhodospiraHalorhodospira group. Some of the species he and his group isolated from hypersaline and haloalkaline environments have become model organisms for the study of the mechanisms of haloadaptation: the functions of three major organic compounds – glycine betaine, ectoine, and trehalose – known to serve as “compatible solutes” in halophilic members of the Bacteria domain, were discovered during studies of these anoxygenic phototrophs. Prof. Trüper’s studies of hypersaline alkaline environments in Egypt also led to the isolation of the first known extremely halophilic archaeon (Natronomonas pharaonis). The guest editors dedicate this special volume of Life to the memory of Prof. Hans Georg Trüper. Full article
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Research

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Open AccessArticle Cloning and Molecular Characterization of an Alpha-Glucosidase (MalH) from the Halophilic Archaeon Haloquadratum walsbyi
Received: 31 August 2017 / Revised: 15 November 2017 / Accepted: 18 November 2017 / Published: 21 November 2017
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Abstract
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated [...] Read more.
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6.0. Enzyme activity values were the highest in the presence of 3 M NaCl or 3–4 M KCl. However, specific activity values were two-fold higher in the presence of 3–4 M KCl when compared to NaCl suggesting a cytoplasmic localization. Phylogenetic analyses, with respect to other alpha-glucosidases from members of the class Halobacteria, showed that the Hqr. walsbyi MalH was most similar (up to 41%) to alpha-glucosidases and alpha-xylosidases of Halorubrum. Moreover, computational analyses for the detection of functional domains, active and catalytic sites, as well as 3D structural predictions revealed a close relationship with an E. coli YicI-like alpha-xylosidase of the GH31 family. However, the purified enzyme did not show alpha-xylosidase activity. This narrower substrate range indicates a discrepancy with annotations from different databases and the possibility of specific substrate adaptations of halophilic glucosidases due to high salinity. To our knowledge, this is the first report on the characterization of an alpha-glucosidase from the halophilic Archaea, which could serve as a new model to gain insights into carbon metabolism in this understudied microbial group. Full article
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Open AccessArticle Arsenite as an Electron Donor for Anoxygenic Photosynthesis: Description of Three Strains of Ectothiorhodospira from Mono Lake, California and Big Soda Lake, Nevada
Received: 5 October 2016 / Revised: 20 December 2016 / Accepted: 21 December 2016 / Published: 26 December 2016
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Abstract
Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring [...] Read more.
Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243T, and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion. Full article
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Open AccessArticle Screening of a Haloferax volcanii Transposon Library Reveals Novel Motility and Adhesion Mutants
Received: 4 October 2016 / Revised: 4 November 2016 / Accepted: 7 November 2016 / Published: 26 November 2016
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Abstract
Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella—structures required for motility—share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum [...] Read more.
Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella—structures required for motility—share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum and pilus biosynthesis and the mechanisms regulating motility and adhesion in archaea, many questions remain. Therefore, we screened a Haloferax volcanii transposon insertion library for motility mutants using motility plates and adhesion mutants, using an adapted air–liquid interface assay. Here, we identify 20 genes, previously unknown to affect motility or adhesion. These genes include potential novel regulatory genes that will help to unravel the mechanisms underpinning these processes. Both screens also identified distinct insertions within the genomic region lying between two chemotaxis genes, suggesting that chemotaxis not only plays a role in archaeal motility, but also in adhesion. Studying these genes, as well as hypothetical genes hvo_2512 and hvo_2876—also critical for both motility and adhesion—will likely elucidate how these two systems interact. Furthermore, this study underscores the usefulness of the transposon library to screen other archaeal cellular processes for specific phenotypic defects. Full article
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Open AccessArticle Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea
Received: 12 July 2016 / Revised: 12 August 2016 / Accepted: 25 August 2016 / Published: 2 September 2016
Cited by 5 | PDF Full-text (2396 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional [...] Read more.
Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5’ to 3’: TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity. Full article
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Open AccessArticle The Use of a Fractional Factorial Design to Determine the Factors That Impact 1,3-Propanediol Production from Glycerol by Halanaerobium hydrogeniformans
Received: 8 July 2016 / Revised: 11 August 2016 / Accepted: 15 August 2016 / Published: 20 August 2016
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Abstract
In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this [...] Read more.
In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this former commodity a waste product. However, Halanaerobium hydrogeniformans, a haloalkaliphilic bacterium, possesses the metabolic capability to convert glycerol into 1,3-propanediol, a valuable commodity compound, without the need for salt dilution or adjusting pH when grown on this waste. Experiments were performed with different combinations of 24 medium components to determine their impact on the production of 1,3-propanediol by using a fractional factorial design. Tested medium components were selected based on data from the organism’s genome. Analysis of HPLC data revealed enhanced production of 1,3-propanediol with additional glycerol, pH, vitamin B12, ammonium ions, sodium sulfide, cysteine, iron, and cobalt. However, other selected components; nitrate ions, phosphate ions, sulfate ions, sodium:potassium ratio, chloride, calcium, magnesium, silicon, manganese, zinc, borate, nickel, molybdenum, tungstate, copper and aluminum, did not enhance 1,3-propanediol production. The use of a fractional factorial design enabled the quick and efficient assessment of the impact of 24 different medium components on 1,3-propanediol production from glycerol from a haloalkaliphilic bacterium. Full article
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Open AccessArticle AglM and VNG1048G, Two Haloarchaeal UDP-Glucose Dehydrogenases, Show Different Salt-Related Behaviors
Received: 11 July 2016 / Revised: 27 July 2016 / Accepted: 29 July 2016 / Published: 3 August 2016
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Abstract
Haloferax volcanii AglM and Halobacterium salinarum VNG1048G are UDP-glucose dehydrogenases involved in N-glycosylation in each species. Despite sharing >60% sequence identity and the ability of VNG1048G to functionally replace AglM in vivo, these proteins behaved differently as salinity changed. Whereas AglM was [...] Read more.
Haloferax volcanii AglM and Halobacterium salinarum VNG1048G are UDP-glucose dehydrogenases involved in N-glycosylation in each species. Despite sharing >60% sequence identity and the ability of VNG1048G to functionally replace AglM in vivo, these proteins behaved differently as salinity changed. Whereas AglM was active in 2–4 M NaCl, VNG1048G lost much of its activity when salinity dropped below 3 M NaCl. To understand the molecular basis of this phenomenon, each protein was examined by size exclusion chromatrography in 2 M NaCl. Whereas AglM appeared as a dodecamer, VNG1048G was essentially detected as a dodecamer and a dimer. The specific activity of the VNG1048G dodecamer was only a sixth of that of AglM, while the dimer was inactive. As such, not only was the oligomeric status of VNG1048G affected by lowered salinity, so was the behavior of the individual dodecamer subunits. Analyzing surface-exposed residues in homology models of the two UDP-glucose dehydrogenases revealed the more acidic and less basic VNG1048G surface, further explaining the greater salt-dependence of the Hbt. salinarum enzyme. Full article
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Review

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Open AccessReview Probing Saltern Brines with an Oxygen Electrode: What Can We Learn about the Community Metabolism in Hypersaline Systems?
Received: 5 May 2016 / Revised: 2 June 2016 / Accepted: 6 June 2016 / Published: 8 June 2016
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Abstract
We have explored the use of optical oxygen electrodes to study oxygenic photosynthesis and heterotrophic activities in crystallizer brines of the salterns in Eilat, Israel. Monitoring oxygen uptake rates in the dark enables the identification of organic substrates that are preferentially used by [...] Read more.
We have explored the use of optical oxygen electrodes to study oxygenic photosynthesis and heterotrophic activities in crystallizer brines of the salterns in Eilat, Israel. Monitoring oxygen uptake rates in the dark enables the identification of organic substrates that are preferentially used by the community. Addition of glycerol (the osmotic solute synthesized by Dunaliella) or dihydroxyacetone (produced from glycerol by Salinibacter) enhanced respiration rates. Pyruvate, produced from glycerol or from some sugars by certain halophilic Archaea also stimulated community respiration. Fumarate had a sparing effect on respiration, possibly as many halophilic Archaea can use fumarate as a terminal electron acceptor in respiration. Calculating the photosynthetic activity of Dunaliella by monitoring oxygen concentration changes during light/dark incubations is not straightforward as light also affects respiration of some halophilic Archaea and Bacteria due to action of light-driven proton pumps. When illuminated, community respiration of brine samples in which oxygenic photosynthesis was inhibited by DCMU decreased by ~40%. This effect was interpreted as the result of competition between two energy yielding systems: the bacteriorhodopsin proton pump and the respiratory chain of the prokaryotes. These findings have important implications for the interpretation of other published data on photosynthetic and respiratory activities in hypersaline environments. Full article
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