Halophilic Microorganisms

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

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 27651

Special Issue Editor


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Guest Editor
Microbiology and Parasitology, University of Sevilla, Sevilla, Spain
Interests: taxonomy; halophilic microorganism; metagenomic; biodiversity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Halophiles are microorganisms adapted for living at hypersaline environments and other saline products. Most of them belong to the bacteria and archaea domains, and their interest is of special relevance both for their adaptation mechanisms to extreme conditions and for their potential biotechnological applications. In recent years, the isolation and taxonomic characterization of halophiles have allowed us to learn more in detail about their heterogeneity, their metabolic and physiological diversity, or ecological distribution and biodiversity. Culture-independent techniques, such as metagenomics and -omics studies, are particularly providing an incentive these studies on halophiles to continue, as there is still an immense field to explore in this regard.

In this Special Issue of Microorganisms, you are invited to send contributions (original articles as well as reviews) concerning the biology, taxonomy, biodiversity, and biotechnological applications of halophilic microorganisms, as well as using genomic and metagenomic approaches to study microbial communities. Information that will improve our understanding of the role of halophilic microorganisms in hypersaline environments, their adaptation to the environmental conditions, their genetic and functional diversity, and their phylogenetic position is especially welcome.

Dr. Cristina Sánchez-Porro
Guest Editor

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Keywords

  • obligate halophiles
  • bacteria
  • archaea
  • taxonomy and biodiversity
  • biotechnology
  • genomics
  • metagenomics
  • physiology and metabolism
  • hypersaline habitats

Published Papers (9 papers)

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Editorial

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4 pages, 214 KiB  
Editorial
Special Issue “Halophilic Microorganisms”
by Cristina Sánchez-Porro
Microorganisms 2023, 11(3), 690; https://doi.org/10.3390/microorganisms11030690 - 08 Mar 2023
Cited by 1 | Viewed by 1143
Abstract
Hypersaline environments are mainly represented by aquatic systems, such as solar salt ponds or natural salt lakes, as well as by the sediments of these hypersaline aquatic ecosystems and soils with high salt content [...] Full article
(This article belongs to the Special Issue Halophilic Microorganisms)

Research

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19 pages, 4323 KiB  
Article
Morphological Phenotypes, Cell Division, and Gene Expression of Escherichia coli under High Concentration of Sodium Sulfate
by Khanh Nguyen and Pradeep Kumar
Microorganisms 2022, 10(2), 274; https://doi.org/10.3390/microorganisms10020274 - 25 Jan 2022
Cited by 7 | Viewed by 3301
Abstract
Sodium and sulfate ions are among the suggested abundant ions on Europa, a moon of Jupiter. In order to investigate the potential habitability of Europa, we study the effects of sodium sulfate (Na2SO4) on a non-halophilic bacterium by subjecting [...] Read more.
Sodium and sulfate ions are among the suggested abundant ions on Europa, a moon of Jupiter. In order to investigate the potential habitability of Europa, we study the effects of sodium sulfate (Na2SO4) on a non-halophilic bacterium by subjecting Escherichia coli (E. coli) to a wide range of Na2SO4 concentrations (0–1.0 m). We discover that, as the concentration of sodium sulfate increases, the biomass doubling time increases and the cell growth is completely inhibited at 1.0 m Na2SO4. Furthermore, we find that E. coli exhibits three distinct morphological phenotypes—(i) shortened, (ii) normal, and (iii) elongated/filamented cells at 0.6 m and 0.8 m Na2SO4. We have examined the expression of different genes involved in sodium and sulfate transport (nhaA, nhaB, cysZ, sbp), osmotically driven transport of water (aqpZ), sulfate metabolism (cysN), fatty acid production (fabA), and a global transcriptional regulator (osmZ). Our results suggest that the expression of these genes is not affected significantly at high concentrations of sodium sulfate in the exponential growth phase. Using our experimental data and the existing data in the literature, we show that the osmotic pressure difference may play a major role in determining the growth inhibition of E. coli and B. subtilis at high concentrations of salt. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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14 pages, 2140 KiB  
Article
Biomineralization by Extremely Halophilic and Metal-Tolerant Community Members from a Sulfate-Dominated Metal-Rich Environment
by Marie Harpke, Sebastian Pietschmann, Flávio Silva Costa, Clara Gansert, Falko Langenhorst and Erika Kothe
Microorganisms 2022, 10(1), 79; https://doi.org/10.3390/microorganisms10010079 - 31 Dec 2021
Cited by 12 | Viewed by 1955
Abstract
The adaptation to adverse environmental conditions can lead to adapted microbial communities that may be screened for mechanisms involved in halophily and, in this case, metal tolerance. At a former uranium mining and milling site in Seelingstädt, Germany, microbial communities from surface waters [...] Read more.
The adaptation to adverse environmental conditions can lead to adapted microbial communities that may be screened for mechanisms involved in halophily and, in this case, metal tolerance. At a former uranium mining and milling site in Seelingstädt, Germany, microbial communities from surface waters and sediment soils were screened for isolates surviving high salt and metal concentrations. The high salt contents consisted mainly of chloride and sulfate, both in soil and riverbed sediment samples, accompanied by high metal loads with presence of cesium and strontium. The community structure was dominated by Chloroflexi, Proteobacteria and Acidobacteriota, while only at the highest contaminations did Firmicutes and Desulfobacterota reach appreciable percentages in the DNA-based community analysis. The extreme conditions providing high stress were mirrored by low numbers of cultivable strains. Thirty-four extremely halotolerant bacteria (23 Bacillus sp. and another 4 Bacillales, 5 Actinobacteria, and 1 Gamma-Proteobacterium) surviving 25 to 100 mM SrCl2, CsCl, and Cs2SO4 were further analyzed. Mineral formation of strontium- or cesium-struvite could be observed, reducing bioavailability and thereby constituting the dominant metal and salt resistance strategy in this environment. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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12 pages, 2356 KiB  
Article
Characterization of the Proteolytic Activity of a Halophilic Aspergillus reticulatus Strain SK1-1 Isolated from a Solar Saltern
by Dawoon Chung, Woon-Jong Yu, Ji-Yeon Lim, Nam-Seon Kang, Yong-Min Kwon, Grace Choi, Seung-Sub Bae, Kichul Cho and Dae-Sung Lee
Microorganisms 2022, 10(1), 29; https://doi.org/10.3390/microorganisms10010029 - 24 Dec 2021
Cited by 9 | Viewed by 3084
Abstract
Salterns are hypersaline environments that are inhabited by diverse halophilic microorganisms, including fungi. In this study, we isolated a fungal strain SK1-1 from a saltern in the Republic of Korea, which was identified as Asperillus reticulatus. This is the first reported saline-environment-derived [...] Read more.
Salterns are hypersaline environments that are inhabited by diverse halophilic microorganisms, including fungi. In this study, we isolated a fungal strain SK1-1 from a saltern in the Republic of Korea, which was identified as Asperillus reticulatus. This is the first reported saline-environment-derived A. reticulatus that belongs to the Aspergillus penicillioides clade and encompasses xerophilic fungi. SK1-1 was halophilic, obligately requiring NaCl for growth, with a maximum radial growth of 6%–9% (w/v) NaCl. To facilitate the biotechnological application of halophilic fungi, we screened the SK1-1 strain for proteolytic activity. Proteases have widespread applications in food processing, detergents, textiles, and waste treatment, and halophilic proteases can enable protein degradation in high salt environments. We assessed the proteolytic activity of the extracellular crude enzyme of SK1-1 using azocasein as a substrate. The crude protease exhibited maximum activity at 40–50 °C, pH 9.5–10.5, and in the absence of NaCl. It was also able to retain up to 69% of its maximum activity until 7% NaCl. Protease inhibitor assays showed complete inhibition of the proteolytic activity of crude enzymes by Pefabloc® SC. Our data suggest that the halophilic A. reticulatus strain SK1-1 produces an extracellular alkaline serine protease. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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16 pages, 2503 KiB  
Article
Taxogenomic and Metabolic Insights into Marinobacterium ramblicola sp. nov., a New Slightly Halophilic Bacterium Isolated from Rambla Salada, Murcia
by Ana Durán-Viseras, David J. Castro, José Carlos Reina, Victoria Béjar and Fernando Martínez-Checa
Microorganisms 2021, 9(8), 1654; https://doi.org/10.3390/microorganisms9081654 - 03 Aug 2021
Cited by 9 | Viewed by 2502
Abstract
A Gram-negative, motile, rod-shaped bacteria, designated D7T, was isolated by using the dilution-to-extinction method, from a soil sample taken from Rambla Salada (Murcia, Spain). Growth of strain D7T was observed at 15–40 °C (optimum, 37 °C), pH 5–9 (optimum, 7) [...] Read more.
A Gram-negative, motile, rod-shaped bacteria, designated D7T, was isolated by using the dilution-to-extinction method, from a soil sample taken from Rambla Salada (Murcia, Spain). Growth of strain D7T was observed at 15–40 °C (optimum, 37 °C), pH 5–9 (optimum, 7) and 0–7.5% (w/v) NaCl (optimum, 3%). It is facultatively anaerobic. Phylogenetic analysis based on 16S rRNA gene sequence showed it belongs to the genus Marinobacterium. The in silico DDH and ANI against closest Marinobacterium relatives support its placement as a new species within this genus. The major fatty acids of strain D7T were C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol and two uncharacterized lipids. Ubiquinone 8 was the unique isoprenoid quinone detected. The DNA G + C content was 59.2 mol%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic characterization, strain D7T (= CECT 9818T = LMG 31312T) represents a novel species of the genus Marinobacterium for which the name Marinobacterium ramblicola sp. nov. is proposed. Genome-based metabolic reconstructions of strain D7T suggested a heterotrophic and chemolitotrophic lifestyle, as well as the capacity to biosynthetize and catabolize compatible solutes, and to degrade hydrocarbon aromatic compounds. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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18 pages, 3217 KiB  
Article
Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing
by Can Akpolat, Ana Beatriz Fernández, Pinar Caglayan, Baris Calli, Meral Birbir and Antonio Ventosa
Microorganisms 2021, 9(7), 1525; https://doi.org/10.3390/microorganisms9071525 - 17 Jul 2021
Cited by 9 | Viewed by 3084
Abstract
Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate [...] Read more.
Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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16 pages, 1476 KiB  
Article
The Survival of Haloferax mediterranei under Stressful Conditions
by Laura Matarredona, Mónica Camacho, Basilio Zafrilla, Gloria Bravo-Barrales, Julia Esclapez and María-José Bonete
Microorganisms 2021, 9(2), 336; https://doi.org/10.3390/microorganisms9020336 - 08 Feb 2021
Cited by 11 | Viewed by 3234
Abstract
Haloarchaea can survive and thrive under exposure to a wide range of extreme environmental factors, which represents a potential interest to biotechnology. Growth responses to different stressful conditions were examined in the haloarchaeon Haloferax mediterranei R4. It has been demonstrated that this halophilic [...] Read more.
Haloarchaea can survive and thrive under exposure to a wide range of extreme environmental factors, which represents a potential interest to biotechnology. Growth responses to different stressful conditions were examined in the haloarchaeon Haloferax mediterranei R4. It has been demonstrated that this halophilic archaeon is able to grow between 10 and 32.5% (w/v) of sea water, at 32–52 °C, although it is expected to grow in temperatures lower than 32 °C, and between 5.75 and 8.75 of pH. Moreover, it can also grow under high metal concentrations (nickel, lithium, cobalt, arsenic), which are toxic to most living beings, making it a promising candidate for future biotechnological purposes and industrial applications. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis quantified the intracellular ion concentrations of these four metals in Hfx. mediterranei, concluding that this haloarchaeon can accumulate Li+, Co2+, As5+, and Ni2+ within the cell. This paper is the first report on Hfx. mediterranei in which multiple stress conditions have been studied to explore the mechanism of stress resistance. It constitutes the most detailed study in Haloarchaea, and, as a consequence, new biotechnological and industrial applications have emerged. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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16 pages, 1958 KiB  
Article
Bioprospecting for Novel Halophilic and Halotolerant Sources of Hydrolytic Enzymes in Brackish, Saline and Hypersaline Lakes of Romania
by Robert Ruginescu, Ioana Gomoiu, Octavian Popescu, Roxana Cojoc, Simona Neagu, Ioana Lucaci, Costin Batrinescu-Moteau and Madalin Enache
Microorganisms 2020, 8(12), 1903; https://doi.org/10.3390/microorganisms8121903 - 30 Nov 2020
Cited by 40 | Viewed by 3783
Abstract
Halophilic and halotolerant microorganisms represent promising sources of salt-tolerant enzymes that could be used in various biotechnological processes where high salt concentrations would otherwise inhibit enzymatic transformations. Considering the current need for more efficient biocatalysts, the present study aimed to explore the microbial [...] Read more.
Halophilic and halotolerant microorganisms represent promising sources of salt-tolerant enzymes that could be used in various biotechnological processes where high salt concentrations would otherwise inhibit enzymatic transformations. Considering the current need for more efficient biocatalysts, the present study aimed to explore the microbial diversity of five under- or uninvestigated salty lakes in Romania for novel sources of hydrolytic enzymes. Bacteria, archaea and fungi were obtained by culture-based approaches and screened for the production of six hydrolases (protease, lipase, amylase, cellulase, xylanase and pectinase) using agar plate-based assays. Moreover, the phylogeny of bacterial and archaeal isolates was studied through molecular methods. From a total of 244 microbial isolates, 182 (74.6%) were represented by bacteria, 22 (9%) by archaea, and 40 (16.4%) by fungi. While most bacteria synthesized protease and lipase, the most frequent hydrolase produced by fungi was pectinase. The archaeal isolates had limited hydrolytic activity, being able to produce only amylase and cellulase. Among the taxonomically identified isolates, the best hydrolytic activities were observed in halotolerant bacteria belonging to the genus Bacillus and in extremely halophilic archaea of the genera Haloterrigena and Halostagnicola. Therefore, the present study highlights that the investigated lakes harbor various promising species of microorganisms able to produce industrially valuable enzymes. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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Review

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19 pages, 3506 KiB  
Review
Recent Antimicrobial Responses of Halophilic Microbes in Clinical Pathogens
by Henciya Santhaseelan, Vengateshwaran Thasu Dinakaran, Hans-Uwe Dahms, Johnthini Munir Ahamed, Santhosh Gokul Murugaiah, Muthukumar Krishnan, Jiang-Shiou Hwang and Arthur James Rathinam
Microorganisms 2022, 10(2), 417; https://doi.org/10.3390/microorganisms10020417 - 11 Feb 2022
Cited by 10 | Viewed by 3747
Abstract
Microbial pathogens that cause severe infections and are resistant to drugs are simultaneously becoming more active. This urgently calls for novel effective antibiotics. Organisms from extreme environments are known to synthesize novel bioprospecting molecules for biomedical applications due to their peculiar characteristics of [...] Read more.
Microbial pathogens that cause severe infections and are resistant to drugs are simultaneously becoming more active. This urgently calls for novel effective antibiotics. Organisms from extreme environments are known to synthesize novel bioprospecting molecules for biomedical applications due to their peculiar characteristics of growth and physiological conditions. Antimicrobial developments from hypersaline environments, such as lagoons, estuaries, and salterns, accommodate several halophilic microbes. Salinity is a distinctive environmental factor that continuously promotes the metabolic adaptation and flexibility of halophilic microbes for their survival at minimum nutritional requirements. A genetic adaptation to extreme solar radiation, ionic strength, and desiccation makes them promising candidates for drug discovery. More microbiota identified via sequencing and ‘omics’ approaches signify the hypersaline environments where compounds are produced. Microbial genera such as Bacillus, Actinobacteria, Halorubrum and Aspergillus are producing a substantial number of antimicrobial compounds. Several strategies were applied for producing novel antimicrobials from halophiles including a consortia approach. Promising results indicate that halophilic microbes can be utilised as prolific sources of bioactive metabolites with pharmaceutical potentialto expand natural product research towards diverse phylogenetic microbial groups which inhabit salterns. The present study reviews interesting antimicrobial compounds retrieved from microbial sources of various saltern environments, with a discussion of their potency in providing novel drugs against clinically drug-resistant microbes. Full article
(This article belongs to the Special Issue Halophilic Microorganisms)
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