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Ben Abdallah M, Chamkha M, Karray F, Sayadi S. Microbial diversity in polyextreme salt flats and their potential applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:11371-11405. [PMID: 38180652 DOI: 10.1007/s11356-023-31644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.
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Affiliation(s)
- Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia.
| | - Mohamed Chamkha
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, BP 1177, 3018, Sfax, Tunisia
| | - Sami Sayadi
- Biotechnology Program, Center for Sustainable Development, College of Arts and Sciences, Qatar University, 2713, Doha, Qatar
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Tilahun L, Asrat A, Wessel GM, Simachew A. Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments. Results Probl Cell Differ 2024; 71:185-212. [PMID: 37996679 DOI: 10.1007/978-3-031-37936-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.
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Affiliation(s)
- Lulit Tilahun
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Asfawossen Asrat
- Department of Mining and Geological Engineering, Botswana International University of Science and Technology, Palapye, Botswana
- School of Earth Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gary M Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
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Hassani II, Quadri I, Yadav A, Bouchard S, Raoult D, Hacène H, Desnues C. Assessment of diversity of archaeal communities in Algerian chott. Extremophiles 2023; 27:2. [PMID: 36469177 DOI: 10.1007/s00792-022-01287-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Halophilic archaea are the dominant type of microorganisms in hypersaline environments. The diversity of halophilic archaea in Zehrez-Chergui (Saharian chott) was analyzed and compared by both analysis of a library of PCR amplified 16S rRNA genes and by cultivation approach. This work, represents the first of its type in Algeria. A total cell count was estimated at 3.8 × 103 CFU/g. The morphological, biochemical, and physiological characterizations of 45 distinct strains, suggests that all of them might be members of the class Halobacteria. Among stains, 23 were characterized phylogenetically and are related to 6 genera of halophilic archaea.The dominance of the genus Halopiger, has not been reported yet in other hypersaline environments. The 100 clones obtained by the molecular approach, were sequenced, and analyzed. The ribosomal library of 61 OTUs showed that the archaeal diversity included uncultured haloarcheon, Halomicrobium, Natronomonas, Halomicroarcula, Halapricum, Haloarcula, Halosimplex, Haloterrigena, Halolamina, Halorubellus, Halorussus and Halonotius. The results of rarefaction analysis indicated that the analysis of an increasing number of clones would have revealed additional diversity. Surprisingly, no halophilic archaea were not shared between the two approaches. Combining both types of methods was considered the best approach to acquire better information on the characteristics of soil halophilic archaea.
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Affiliation(s)
- Imene Ikram Hassani
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria.
| | - Inès Quadri
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria
| | - Archana Yadav
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sonia Bouchard
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
| | - Didier Raoult
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
| | - Hocine Hacène
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie, USTHB Université, Bab Ezzouar, Algeria
| | - Christelle Desnues
- Faculté de Médecine, Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD 198, Inserm U1095, 27 Boulevard Jean Moulin, 13385, Marseille, France
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Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology. FERMENTATION 2022. [DOI: 10.3390/fermentation8080365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.
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Chen S, Tu D, Hong T, Luo Y, Shen L, Ren P, Lu P, Chen X. Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain. Gene 2022; 841:146766. [PMID: 35908623 DOI: 10.1016/j.gene.2022.146766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/26/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNAThr, tRNAArg, tRNAGly and tRNAAsn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.
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Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
| | - Demei Tu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuqing Luo
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Peng Lu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Saccò M, White NE, Harrod C, Salazar G, Aguilar P, Cubillos CF, Meredith K, Baxter BK, Oren A, Anufriieva E, Shadrin N, Marambio-Alfaro Y, Bravo-Naranjo V, Allentoft ME. Salt to conserve: a review on the ecology and preservation of hypersaline ecosystems. Biol Rev Camb Philos Soc 2021; 96:2828-2850. [PMID: 34747117 DOI: 10.1111/brv.12780] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/01/2023]
Abstract
When it comes to the investigation of key ecosystems in the world, we often omit salt from the ecological recipe. In fact, despite occupying almost half of the volume of inland waters and providing crucial services to humanity and nature, inland saline ecosystems are often overlooked in discussions regarding the preservation of global aquatic resources of our planet. As a result, our knowledge of the biological and geochemical dynamics shaping these environments remains incomplete and we are hesitant in framing effective protective strategies against the increasing natural and anthropogenic threats faced by such habitats. Hypersaline lakes, water bodies where the concentration of salt exceeds 35 g/l, occur mainly in arid and semiarid areas resulting from hydrological imbalances triggering the accumulation of salts over time. Often considered the 'exotic siblings' within the family of inland waters, these ecosystems host some of the most extremophile communities worldwide and provide essential habitats for waterbirds and many other organisms in already water-stressed regions. These systems are often highlighted as natural laboratories, ideal for addressing central ecological questions due to their relatively low complexity and simple food web structures. However, recent studies on the biogeochemical mechanisms framing hypersaline communities have challenged this archetype, arguing that newly discovered highly diverse communities are characterised by specific trophic interactions shaped by high levels of specialisation. The main goal of this review is to explore our current understanding of the ecological dynamics of hypersaline ecosystems by addressing four main research questions: (i) why are hypersaline lakes unique from a biological and geochemical perspective; (ii) which biota inhabit these ecosystems and how have they adapted to the high salt conditions; (iii) how do we protect biodiversity from increasing natural and anthropogenic threats; and (iv) which scientific tools will help us preserve hypersaline ecosystems in the future? First, we focus on the ecological characterisation of hypersaline ecosystems, illustrate hydrogeochemical dynamics regulating such environments, and outline key ecoregions supporting hypersaline systems across the globe. Second, we depict the diversity and functional aspects of key taxa found in hypersaline lakes, from microorganisms to plants, invertebrates, waterbirds and upper trophic levels. Next, we describe ecosystem services and discuss possible conservation guidelines. Finally, we outline how cutting-edge technologies can provide new insights into the study of hypersaline ecology. Overall, this review sheds further light onto these understudied ecosystems, largely unrecognised as important sources of unique biological and functional diversity. We provide perspectives for key future research avenues, and advocate that the conservation of hypersaline lakes should not be taken with 'a grain of salt'.
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Affiliation(s)
- Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Gonzalo Salazar
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Pablo Aguilar
- Núcleo Milenio INVASAL, Concepción, 3349001, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Carolina F Cubillos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, U.S.A
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, the Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Elena Anufriieva
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Nickolai Shadrin
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Yeri Marambio-Alfaro
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Víctor Bravo-Naranjo
- Facultad de Ciencias, Universidad de La Serena, Benavente 980, La Serena, Coquimbo, Chile
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia.,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing. Microorganisms 2021; 9:microorganisms9071525. [PMID: 34361960 PMCID: PMC8304926 DOI: 10.3390/microorganisms9071525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 01/31/2023] Open
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 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.
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Halophilic Prokaryotes in Urmia Salt Lake, a Hypersaline Environment in Iran. Curr Microbiol 2021; 78:3230-3238. [PMID: 34216240 DOI: 10.1007/s00284-021-02583-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/14/2021] [Indexed: 10/20/2022]
Abstract
In this study, fluorescence in situ hybridization (FISH) and PCR-amplified fragments of the 16SrDNA gene were used to determine prokaryotes diversity in Urmia Salt Lake. Prokaryote cell population in Urmia lake range from 3.1 ± 0.3 × 106, 2 ± 0.2 × 108, 4 ± 0.3 × 108, and 1.8 ± 0.2 × 108 cells ml-1 for water, soil, sediment, and salt samples by DAPI (4́, 6-diamidino-2-phenylindole) direct count, respectively. The proportion of bacteria and archaea in the samples determinable by FISH ranged between 36.1 and 55% and 48.5 and 55.5%, respectively. According to the DGGE method, some bands were selected and separated from the gel, then amplified and sequenced. The results of sequences were related to two phyla Proteobacteria (16.6%) and Bacteroidetes (83.3%), which belonged to four genera Salinibacter, Mangroviflexus, Pseudomonas, and Cesiribacter, and the archaeal sequences were related to Euryarchaeota phyla and three genera Halonotius, Haloquadratum, and Halorubrum. According to our results, it seems that prokaryotic populations in this hypersaline environment are more diverse than expected, and bacteria are so abundant and diverse and form the metabolically active part of the microbial population inhabiting this extreme environment. Molecular dependent and independent approaches revealed a different aspect of this environment microbiota.
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Bioprospecting potentials of moderately halophilic bacteria and the isolation of squalene producers from Kuwait sabkha. Int Microbiol 2021; 24:373-384. [PMID: 33755814 DOI: 10.1007/s10123-021-00173-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
Sabkhas in Kuwait are unique hypersaline marine environments under-explored for bacterial community composition and bioprospecting. The 16S rRNA sequence analysis of 46 isolates with distinct morphology from two Kuwait sabkhas recovered 11 genera. Phylum Firmicutes dominated these isolates, and Bacillus (32.6%) was recovered as the dominant genera, followed by Halococcus (17.4%). These isolates were moderately halophilic, and some of them showed tolerance and growth at extreme levels of salt (20%), pH (5 and/or 11), and temperature (55 °C). A higher percentage of isolates harbored protease (63.0), followed by DNase (41.3), amylase (41.3), and lipase (32.6). Selected isolates showed antimicrobial activity against E. faecalis and isolated Halomonas shengliensis, and Idiomarina piscisalsi harbored gene coding for dNDP-glucose 4,6-dehydratase (Glu 1), indicating their potential to produce biomolecules with deoxysugar moieties. Palmitic acid or oleic acid was the dominant fatty acid, and seven isolates had some polyunsaturated fatty acids (linolenic or γ-linolenic acid). Interestingly, six isolates belonging to Planococcus and Oceanobacillus genus produced squalene, a bioactive isoprenoid molecule. Their content increased 30-50% in the presence of Terbinafine. The potential bioactivities and extreme growth conditions make this untapped bacterial diversity a promising candidate for future bioprospecting studies.
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Çınar S, Mutlu MB. Prokaryotic Community Compositions of the Hypersaline Sediments of Tuz Lake Demonstrated by Cloning and High-Throughput Sequencing. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Fatholahpoor Kami K, Ghane M, Babaeekhou L. Hydrolase-Producing Moderately Halophilic Bacteria from Eshtehard Desert (Iran). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Mani K, Taib N, Hugoni M, Bronner G, Bragança JM, Debroas D. Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India. Front Microbiol 2020; 11:1891. [PMID: 33013726 PMCID: PMC7461921 DOI: 10.3389/fmicb.2020.01891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/20/2020] [Indexed: 11/26/2022] Open
Abstract
The microbial fluctuations along an increasing salinity gradient during two different salt production phases – initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes on Illumina MiSeq platform. Elemental analysis of the brine samples showed high concentration of sodium (Na+) and chloride (Cl–) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea transited from sediment to brine while Bacteria transited from brine to sediment with increasing salinity. Frequency of Archaea was found to be significantly enriched even in low and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence frequency of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.
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Affiliation(s)
- Kabilan Mani
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Zuarinagar, India.,Center for Molecular Medicine & Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Najwa Taib
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Gisele Bronner
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Judith M Bragança
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Zuarinagar, India
| | - Didier Debroas
- UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement (LMGE), Université Clermont Auvergne, Clermont-Ferrand, France
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13
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Glamoclija M, Ramirez S, Sirisena K, Widanagamage I. Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico. Front Microbiol 2019; 10:2595. [PMID: 31781077 PMCID: PMC6861310 DOI: 10.3389/fmicb.2019.02595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/25/2019] [Indexed: 01/23/2023] Open
Abstract
The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.
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Affiliation(s)
- Mihaela Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States
| | - Steven Ramirez
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States
| | - Kosala Sirisena
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States.,Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, United States.,Department of Environmental Technology, Faculty of Technology, University of Colombo, Colombo, Sri Lanka
| | - Inoka Widanagamage
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, United States.,Department of Geology and Geological Engineering, The University of Mississippi, Oxford, MS, United States
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14
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Satari Faghihi L, Seyedalipour B, Ahmady-asbchin S, Riazi G. Moderately Halophilic Bacteria and Their Industrially Important Enzymes from the Ancient Ecosystem Badab-e Surt. Ind Biotechnol (New Rochelle N Y) 2019. [DOI: 10.1089/ind.2018.0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Leila Satari Faghihi
- University of Mazandaran, Department of Molecular and Cell Biology, Babolsar, Iran
| | - Bagher Seyedalipour
- University of Mazandaran, Department of Molecular and Cell Biology, Babolsar, Iran
| | | | - Gholamhossein Riazi
- University of Tehran, Institute of Biochemistry and Biophysics, Biochemistry Department, Tehran, Iran
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15
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Exopolysaccharides and Biofilms in Mitigating Salinity Stress: The Biotechnological Potential of Halophilic and Soil-Inhabiting PGPR Microorganisms. SOIL BIOLOGY 2019. [DOI: 10.1007/978-3-030-18975-4_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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16
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Lee CJD, McMullan PE, O'Kane CJ, Stevenson A, Santos IC, Roy C, Ghosh W, Mancinelli RL, Mormile MR, McMullan G, Banciu HL, Fares MA, Benison KC, Oren A, Dyall-Smith ML, Hallsworth JE. NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats. FEMS Microbiol Rev 2018; 42:672-693. [PMID: 29893835 DOI: 10.1093/femsre/fuy026] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/08/2018] [Indexed: 11/12/2022] Open
Abstract
NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.
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Affiliation(s)
- Callum J D Lee
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Phillip E McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Callum J O'Kane
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Inês C Santos
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Rocco L Mancinelli
- BAER Institute, Mail Stop 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Melanie R Mormile
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65401, USA
| | - Geoffrey McMullan
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Mario A Fares
- Department of Abiotic Stress, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia 46022, Spain.,Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de Valencia (CSIC-UV), Valencia, 46980, Spain.,Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Dublin, Ireland
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV 26506-6300, USA
| | - Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 9190401, Israel
| | - Mike L Dyall-Smith
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland
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17
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Hugoni M, Escalas A, Bernard C, Nicolas S, Jézéquel D, Vazzoler F, Sarazin G, Leboulanger C, Bouvy M, Got P, Ader M, Troussellier M, Agogué H. Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Mol Ecol 2018; 27:4775-4786. [DOI: 10.1111/mec.14901] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Mylène Hugoni
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Arthur Escalas
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Cécile Bernard
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Sébastien Nicolas
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Fanny Vazzoler
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | | | - Marc Bouvy
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Patrice Got
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Magali Ader
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Marc Troussellier
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Hélène Agogué
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
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18
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Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays. Extremophiles 2018; 22:811-823. [DOI: 10.1007/s00792-018-1040-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/09/2018] [Indexed: 11/26/2022]
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19
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de la Haba RR, Corral P, Sánchez-Porro C, Infante-Domínguez C, Makkay AM, Amoozegar MA, Ventosa A, Papke RT. Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure. Front Microbiol 2018; 9:512. [PMID: 29662474 PMCID: PMC5890160 DOI: 10.3389/fmicb.2018.00512] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH). 16S rRNA gene sequence could not differentiate the newly isolated strains from described species, while MLSA grouped strains into three major clusters. Two of those MLSA clusters distinguished candidates for new species. The third cluster with concatenated sequence identity equal to or greater than 97.5% was comprised of strains from Aran-Bidgol Lake (Iran) and solar salterns in Namibia and Spain, and two previously described species isolated from Mexico and Algeria. PLP and DDH analyses showed that Aran-Bidgol strains formed uniform populations, and that strains isolated from other geographic locations were heterogeneous and divergent, indicating that they may constitute different species. Therefore, applying only sequencing approaches and similarity cutoffs for circumscribing species may be too conservative, lumping concealed diversity into a single taxon. Further, our data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.
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Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Carmen Infante-Domínguez
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Andrea M. Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Mohammad A. Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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20
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Papizadeh M, Wijayawardene NN, Amoozegar MA, Saba F, Fazeli SAS, Hyde KD. Neocamarosporium jorjanensis, N. persepolisi, and N. solicola spp. nov. (Neocamarosporiaceae, Pleosporales) isolated from saline lakes of Iran indicate the possible halotolerant nature for the genus. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1341-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Abstract
Lake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg−1 salinity brine, a red ~180 g kg−1 salinity brine and a white ~300 g kg−1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.
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22
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Kambourova M, Tomova I, Boyadzhieva I, Radchenkova N, Vasileva-Tonkova E. Phylogenetic analysis of the bacterial community in a crystallizer pond, Pomorie salterns, Bulgaria. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1265900] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Margarita Kambourova
- Laboratory of Extremophilic Bacteria, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iva Tomova
- Laboratory of Extremophilic Bacteria, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ivanka Boyadzhieva
- Laboratory of Extremophilic Bacteria, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Nadja Radchenkova
- Laboratory of Extremophilic Bacteria, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Evgenia Vasileva-Tonkova
- Laboratory of Extremophilic Bacteria, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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23
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Di Meglio L, Santos F, Gomariz M, Almansa C, López C, Antón J, Nercessian D. Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns. FEMS Microbiol Ecol 2016; 92:fiw184. [PMID: 27604253 DOI: 10.1093/femsec/fiw184] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 11/13/2022] Open
Abstract
Seasonal sampling was carried out at three Argentinian salterns, Salitral Negro (SN), Colorada Grande (CG) and Guatraché (G), to analyze abiotic parameters and microbial diversity and dynamics. Microbial assemblages were correlated to environmental factors by statistical analyses. Principal component analysis of the environmental data grouped SN and CG samples separately from G samples owing to G's higher pH values and sulfate concentration. Differences in microbial assemblages were also found. Many archaeal sequences belonged to uncultured members of Haloquadratum and Haloquadratum-related genera, with different environmental optima. Notably, nearly half of the archaeal sequences were affiliated to the recently described 'Candidatus Haloredividus' (phylum Nanohaloarchaeota), not previously detected in salt-saturated environments. Most bacterial sequences belonged to Salinibacter representatives, while sequences affiliated to the recently described genus Spiribacter were also found. Seasonal analysis showed at least 40% of the microbiota from the three salterns was prevalent through the year, indicating they are well adapted to environmental fluctuations. On the other hand, a minority of archaeal and bacterial sequences were found to be seasonally distributed. Five viral morphotypes and also eukaryal predators were detected, suggesting different mechanisms for controlling prokaryotic numbers. Notably, Guatraché was the saltern that harbored the highest virus-to-cell ratios reported to date for hypersaline environments.
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Affiliation(s)
- Leonardo Di Meglio
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, UNMDP - CONICET, Funes 3250 4° nivel, 7600 Mar del Plata, Argentina
| | - Fernando Santos
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - María Gomariz
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - Cristina Almansa
- Servicios Técnicos de Investigación (SSTTI), Unidad de Microscopía, Universidad de Alicante, Alicante, 03690 San Vicente del Raspeig, España
| | - Cristina López
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, 03690 San Vicente del Raspeig, España
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, UNMDP - CONICET, Funes 3250 4° nivel, 7600 Mar del Plata, Argentina
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24
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Nigro LM, Hyde AS, MacGregor BJ, Teske A. Phylogeography, Salinity Adaptations and Metabolic Potential of the Candidate Division KB1 Bacteria Based on a Partial Single Cell Genome. Front Microbiol 2016; 7:1266. [PMID: 27597842 PMCID: PMC4993014 DOI: 10.3389/fmicb.2016.01266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/02/2016] [Indexed: 01/15/2023] Open
Abstract
Deep-sea hypersaline anoxic basins and other hypersaline environments contain abundant and diverse microbial life that has adapted to these extreme conditions. The bacterial Candidate Division KB1 represents one of several uncultured groups that have been consistently observed in hypersaline microbial diversity studies. Here we report the phylogeography of KB1, its phylogenetic relationships to Candidate Division OP1 Bacteria, and its potential metabolic and osmotic stress adaptations based on a partial single cell amplified genome of KB1 from Orca Basin, the largest hypersaline seafloor brine basin in the Gulf of Mexico. Our results are consistent with the hypothesis – previously developed based on 14C incorporation experiments with mixed-species enrichments from Mediterranean seafloor brines – that KB1 has adapted its proteins to elevated intracellular salinity, but at the same time KB1 apparently imports glycine betaine; this compatible solute is potentially not limited to osmoregulation but could also serve as a carbon and energy source.
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Affiliation(s)
- Lisa M Nigro
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Andrew S Hyde
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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25
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Rasooli M, Amoozegar MA, Akhavan Sepahy A, Babavalian H, Tebyanian H. Isolation, Identification and Extracellular Enzymatic Activity of Culturable Extremely Halophilic Archaea and Bacteria of IncheBoroun Wetland. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2016. [DOI: 10.56431/p-2e1v3s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Extremely halophilic diversity of IncheBroun wetland located in the north of Iran was investigated by using culture-dependent methods. Sampling was carried out in May and September 2014. In each sampling 4 distinct regions of wetland were analyzed by using complex media like MGM, JCM168, MH1 and an alkaliphilic medium containing 23% salts. After incubation at 40°C, a total of 406 isolates and 2.1 × 106 CFU/ml were obtained in culture media. Among them 361 isolates were obtained from MGM and 39 isolates from JCM 168, 3 isolates from MH1 and 3 isolates from the alkaliphilic media. Initial morphological, biochemical and physiological tests were performed. Production of 4 hydrolytic enzymes by 45 selected strains was assayed qualitatively. A total of 38, 19 and 6 strains were able to produce lipase, DNase and amylase activity. Protease activity was not observed among strains. As total 45 strains were selected randomly and phylogenetic analysis of 16S rRNA was performed for them. Among selected strains 40 isolated strians belonged to Haloarchaea and were belonged to the genera: Haloarcula(30%), Halorubrum(27.5%), Haloferax(17.5%), Halobellus (10%), Halogeometricum(5.2%), Halobacterium(2.6%), Halolamina(2.6%), Halorhabdus (2.6%) and Halostagnicola (2.6%). Haloarcula and Halorubrum were the dominant populations. A total of 5 strains belonged to domain of Bacteria and were similar to members of Rhodovibrio (40%), Pseudomonas (40%) and Salicola (20%).
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26
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Rasooli M, Amoozegar MA, Akhavan Sepahy A, Babavalian H, Tebyanian H. Isolation, Identification and Extracellular Enzymatic Activity of Culturable Extremely Halophilic Archaea and Bacteria of IncheBoroun Wetland. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2016. [DOI: 10.18052/www.scipress.com/ilns.56.40] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Extremely halophilic diversity of IncheBroun wetland located in the north of Iran was investigated by using culture-dependent methods. Sampling was carried out in May and September 2014. In each sampling 4 distinct regions of wetland were analyzed by using complex media like MGM, JCM168, MH1 and an alkaliphilic medium containing 23% salts. After incubation at 40°C, a total of 406 isolates and 2.1 × 106CFU/ml were obtained in culture media. Among them 361 isolates were obtained from MGM and 39 isolates from JCM 168, 3 isolates from MH1 and 3 isolates from the alkaliphilic media. Initial morphological, biochemical and physiological tests were performed. Production of 4 hydrolytic enzymes by 45 selected strains was assayed qualitatively. A total of 38, 19 and 6 strains were able to produce lipase, DNase and amylase activity. Protease activity was not observed among strains. As total 45 strains were selected randomly and phylogenetic analysis of 16S rRNA was performed for them. Among selected strains 40 isolated strians belonged to Haloarchaea and were belonged to the genera:Haloarcula(30%),Halorubrum(27.5%),Haloferax(17.5%),Halobellus(10%),Halogeometricum(5.2%),Halobacterium(2.6%),Halolamina(2.6%),Halorhabdus(2.6%) andHalostagnicola(2.6%).HaloarculaandHalorubrumwere the dominant populations. A total of 5 strains belonged to domain ofBacteriaand were similar to members ofRhodovibrio(40%),Pseudomonas(40%) andSalicola(20%).
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27
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Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey). Extremophiles 2016; 20:589-601. [PMID: 27306996 DOI: 10.1007/s00792-016-0845-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
The prokaryotic communities of four salterns (Bingöl, Fadlum, Kemah, and Tuzlagözü) in Turkey were examined and compared using the cultivation and cultivation-independent methods [fluorescence in situ hybridization (FISH) and 454 pyrosequencing]. FISH analysis with universal probes revealed that feeding waters carried 1.6 × 10(2)-1.7 × 10(3) cells mL(-1), while crystallization ponds carried 3.8 × 10(6)-2.0 × 10(7) cells mL(-1) that were mostly haloarchaea, including square cells (except for Kemah). High-throughput 16S rRNA-based gene sequencing showed that the most frequent archaeal OTUs in Bingöl, Fadlum, Tuzlagözü, and Kemah samples were affiliated with Haloquadratum (76.8 %), Haloarcula (27.8 %), Halorubrum (49.6 %), and Halonotius (59.8 %), respectively. Bacteroidetes was the dominant bacterial phylum in Bingöl and Fadlum, representing 71.5 and 79.5 % of the bacterial OTUs (respectively), while the most abundant bacterial phylum found in the Kemah saltern was Proteobacteria (79.6 %). The majority of the bacterial OTUs recovered from Tuzlagözü belonged to the Cyanobacteria (35.7 %), Bacteroidetes (35.0 %), and Proteobacteria (25.5 %) phyla. Cultivation studies revealed that the archaeal isolates were closely related to the genera Halobacterium, Haloarcula, and Halorubrum. Bacterial isolates were confined to two phyla, Proteobacteria (Alphaproteobacteria and Gammaproteobacteria classes) and Bacteroidetes. Comparative analysis showed that members of the Euryarchaeota, Bacteroidetes, Proteobacteria, and Cyanobacteria phyla were major inhabitants of the solar salterns.
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Abdallah MB, Karray F, Mhiri N, Mei N, Quéméneur M, Cayol JL, Erauso G, Tholozan JL, Alazard D, Sayadi S. Prokaryotic diversity in a Tunisian hypersaline lake, Chott El Jerid. Extremophiles 2016; 20:125-38. [PMID: 26724953 DOI: 10.1007/s00792-015-0805-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/06/2015] [Indexed: 11/30/2022]
Abstract
Prokaryotic diversity was investigated in a Tunisian salt lake, Chott El Jerid, by quantitative real-time PCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting methods targeting the 16S rRNA gene and culture-dependent methods. Two different samples S1-10 and S2-10 were taken from under the salt crust of Chott El Jerid in the dry season. DGGE analysis revealed that bacterial sequences were related to Firmicutes, Proteobacteria, unclassified bacteria, and Deinococcus-Thermus phyla. Anaerobic fermentative and sulfate-reducing bacteria were also detected in this ecosystem. Within the domain archaea, all sequences were affiliated to Euryarchaeota phylum. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of bacteria was 5 × 10(6) DNA copies g(-1) whereas archaea varied between 5 × 10(5) and 10(6) DNA copies g(-1) in these samples. Eight anaerobic halophilic fermentative bacterial strains were isolated and affiliated with the species Halanaerobium alcaliphilum, Halanaerobium saccharolyticum, and Sporohalobacter salinus. These data showed an abundant and diverse microbial community detected in the hypersaline thalassohaline environment of Chott El Jerid.
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Affiliation(s)
- Manel Ben Abdallah
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Fatma Karray
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia. .,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia.
| | - Najla Mhiri
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia
| | - Nan Mei
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Marianne Quéméneur
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Jean-Luc Cayol
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Gaël Erauso
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France.,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia
| | - Jean-Luc Tholozan
- IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Didier Alazard
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,IRD, University of Aix-Marseille, University of Toulon, CNRS, MIO, UM 110, 13288, Marseille Cedex 09, France
| | - Sami Sayadi
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Route Sidi Mansour, km 6, BP 1177, 3018, Sfax, Tunisia.,Laboratoire Mixte International « Contaminants et Ecosystèmes Marins Sud Méditerranéens » (LMI COSYS-Med), Sfax, Tunisia
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29
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
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30
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Corral P, de la Haba RR, Sánchez-Porro C, Ali Amoozegar M, Thane Papke R, Ventosa A. Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake. Int J Syst Evol Microbiol 2015; 66:435-444. [PMID: 26537912 DOI: 10.1099/ijsem.0.000738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two extremely halophilic archaea, strains Cb34T and C170, belonging to the genus Halorubrum, were isolated from the brine of the hypersaline lake Aran-Bidgol in Iran. Cells of the two strains were motile, pleomorphic rods, stained Gram-variable and produced red-pigmented colonies. Strains Cb34T and C170 required 25 % (w/v) salts, pH 7.0 and 37 °C for optimal growth under aerobic conditions; 0.3 M Mg2+ was required. Cells of both isolates were lysed in distilled water and hypotonic treatment with < 10 % NaCl provoked cell lysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that these two strains were closely related to Halorubrum cibi B31T (98.8 %) and other members of the genus Halorubrum. In addition, studies based on the rpoB' gene revealed that strains Cb34T and C170 are placed among the species of Halorubrum and are closely related to Halorubrum cibi B31T, with rpoB' gene sequence similarity less than or equal to 95.7 %. The polar lipid patterns of both strains consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 62.1-62.4 mol%. DNA-DNA hybridization studies confirmed that strains Cb34T and C170 constitute a distinct species. Data obtained in this study show that the two strains represent a novel species, for which the name Halorubrum halodurans sp. nov. is proposed. The type strain is Cb34T ( = CECT 8745T = IBRC-M 10233T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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31
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Corral P, de la Haba RR, Sánchez-Porro C, Amoozegar MA, Papke RT, Ventosa A. Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake. Int J Syst Evol Microbiol 2015; 65:1770-1778. [PMID: 25744586 DOI: 10.1099/ijs.0.000175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely halophilic archaeon belonging to the genus Halorubrum, strain C49T, was isolated from sediment of the hypersaline lake Aran-Bidgol in Iran. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain C49T was closely related to Halorubrum saccharovorum JCM 8865T (99.5 %) and other species of the genus Halorubrum. Studies based on multilocus sequence analysis revealed that strain C49T is placed among the species of Halorubrum; the strain constituted a defined branch in comparison with the type strains of species of Halorubrum, while the 16S rRNA gene sequence divergence could not define the status of the newly isolated strain. For optimum growth, strain C49T required 20 % (w/v) salts at pH 7.0 and 37 °C under aerobic conditions. Mg2+ was not required. The cells were pleomorphic rods, motile and stained Gram-variable. Colonies of the strain were pink. Hypotonic treatment with <12 % NaCl provoked cell lysis. The polar lipid pattern of strain C49T consisted of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester derived from both C20C20 and C20C25 archaeol, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The DNA G+C content was 64.2 mol%. DNA-DNA hybridization studies and average nucleotide identity confirmed that strain C49T constitutes a distinct genospecies. Data obtained in this study show that strain C49T represents a novel species, for which the name Halorubrum persicum sp. nov. is proposed. The type strain is C49T ( = IBRC-M 10232T = JCM 30541T).
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Affiliation(s)
- Paulina Corral
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Mohammad Ali Amoozegar
- Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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32
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Culturable diversity of aerobic halophilic archaea (Fam. Halobacteriaceae) from hypersaline, meromictic Transylvanian lakes. Extremophiles 2015; 19:525-37. [DOI: 10.1007/s00792-015-0738-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/27/2015] [Indexed: 10/24/2022]
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33
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Yakimov MM, La Cono V, Spada GL, Bortoluzzi G, Messina E, Smedile F, Arcadi E, Borghini M, Ferrer M, Schmitt-Kopplin P, Hertkorn N, Cray JA, Hallsworth JE, Golyshin PN, Giuliano L. Microbial community of the deep-sea brine LakeKryosseawater-brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA. Environ Microbiol 2015; 17:364-82. [DOI: 10.1111/1462-2920.12587] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/31/2014] [Indexed: 01/14/2023]
Affiliation(s)
| | - Violetta La Cono
- CNR; Institute for Coastal Marine Environment; Messina 98122 Italy
| | - Gina L. Spada
- CNR; Institute for Coastal Marine Environment; Messina 98122 Italy
| | | | - Enzo Messina
- CNR; Institute for Coastal Marine Environment; Messina 98122 Italy
| | | | - Erika Arcadi
- CNR; Institute for Coastal Marine Environment; Messina 98122 Italy
| | | | | | - Phillippe Schmitt-Kopplin
- Analytical BioGeoChemistry; Helmholtz Zentrum München; German Research Center for Environmental Health; Neuherberg Germany
- Analytical Food Chemistry; Technische Universität München; Freising-Weihenstephan Germany
| | - Norbert Hertkorn
- Analytical BioGeoChemistry; Helmholtz Zentrum München; German Research Center for Environmental Health; Neuherberg Germany
| | - Jonathan A. Cray
- Institute for Global Food Security; School of Biological Sciences; MBC; Queen's University Belfast; Belfast BT9 7BL Northern Ireland
| | - John E. Hallsworth
- Institute for Global Food Security; School of Biological Sciences; MBC; Queen's University Belfast; Belfast BT9 7BL Northern Ireland
| | - Peter N. Golyshin
- School of Biological Sciences; Bangor University; Bangor Gwynedd LL57 2UW UK
| | - Laura Giuliano
- CNR; Institute for Coastal Marine Environment; Messina 98122 Italy
- Mediterranean Science Commission (CIESM); MC 98000 Monaco
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34
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Wang J, Wang F, Chu L, Wang H, Zhong Z, Liu Z, Gao J, Duan H. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin. PLoS One 2014; 9:e112812. [PMID: 25401703 PMCID: PMC4234628 DOI: 10.1371/journal.pone.0112812] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 10/19/2014] [Indexed: 12/21/2022] Open
Abstract
Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.
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Affiliation(s)
- Jiali Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Institute of Shandong River Wetlands, Laiwu, China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- * E-mail:
| | - Limin Chu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Hydrology and Water Resource, Hohai University, Nanjing, China
| | - Hao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Zhiping Zhong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhipei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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35
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Amoozegar MA, Bagheri M, Didari M, Mehrshad M, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov. Int J Syst Evol Microbiol 2014; 64:3616-3623. [DOI: 10.1099/ijs.0.065375-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6BT, was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6BT were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6BT was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5–20.0 % (w/v), with optimum growth occurring at 10.0 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6BT was shown to belong to the phylum
Firmicutes
and its closest phylogenetic similarities were with the species
Virgibacillus koreensis
BH30097T (97.5 %),
Virgibacillus albus
YIM 93624T (97.4 %),
Sediminibacillus halophilus
EN8dT (96.8 %),
Sediminibacillus albus
NHBX5T (96.6 %),
Virgibacillus carmonensis
LMG 20964T (96.3 %) and
Paraliobacillus quinghaiensis
YIM-C158T (96.0 %), respectively. Phylogenetic analysis revealed that strain B6BT, along with
V. koreensis
BH30097T and
V. albus
YIM 93624T, clustered in a separate clade in the family
Bacillaceae
. The DNA G+C content of the novel isolate was 35.8 mol%. DNA–DNA hybridization experiments revealed low levels of relatedness between strain B6BTand
V. koreensis
BH30097T (13 %) and
V. albus
YIM 93624T (33 %). The major cellular fatty acid of strain B6BT was anteiso-C15 : 0 (75.1 %) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90 %) and MK-6 (3 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6BT within the phylum
Firmicutes
. It is closely related to
V. koreensis
and
V. albus
, but with features that clearly distinguish it from species of the genus
Virgibacillus
or of other related genera. On the basis of the polyphasic evidence derived in this study, we propose that strain B6BT be placed within a new genus, as Aquibacillus halophilus gen. nov., sp. nov., with B6BT as the type strain ( = IBRC-M 10775T = KCTC 13828T). We also propose that
V. koreensis
and
V. albus
should be transferred to this new genus and be named Aquibacillus koreensis comb. nov. and Aquibacillus albus comb. nov., respectively. The type strain of Aquibacillus koreensis comb. nov. is BH30097T ( = KCTC 3823T = IBRC-M 10657T = JCM 12387T) and the type strain of Aquibacillus albus comb. nov. is YIM 93624T ( = DSM 23711T = IBRC-M 10798T = JCM 17364T).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Bagheri
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Maryam Didari
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maliheh Mehrshad
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Han D, Cui HL. Halobacterium rubrum sp. nov., isolated from a marine solar saltern. Arch Microbiol 2014; 196:847-51. [DOI: 10.1007/s00203-014-1023-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/12/2014] [Accepted: 07/31/2014] [Indexed: 12/16/2022]
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Babavalian H, Amoozegar MA, Zahraei S, Rohban R, Shakeri F, Moghaddam MM. Comparison of bacterial biodiversity and enzyme production in three hypersaline lakes; urmia, howz-soltan and aran-bidgol. Indian J Microbiol 2014; 54:444-9. [PMID: 25320444 DOI: 10.1007/s12088-014-0481-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/06/2014] [Indexed: 11/24/2022] Open
Abstract
This research is a comparative study on the diversity of halophilic bacteria with hydrolytic activities in three significant hypersaline lakes; Urmia in the northwest and Howz-Soltan and Aran-Bidgol in the central desert in Iran. Isolated strains from these saline lakes were found to be halotolerant, moderately and extremely halophilic bacteria. The bacteria in each saline lake were able to produce different hydrolytic enzymes including amylase, protease, lipase, DNase, inulinase, xylanase, carboxy methyl cellulase, pectinase and pullulanase. 188, 302, 91 halophilic strains were isolated from Urmia Lake, Howz-Soltan and Aran-Bidgol playa, respectively. The numbers of Gram-positive strains were more than Gram-negatives, and among Gram-positive bacteria; spore-forming bacilli were most abundant. Due to the unique physico-chemical conditions of the lake environments, the hydrolytic activities of isolated strains were significantly different. For instance, isolated strains from Howz-Soltan playa did not produce pectinase, DNase, amylase, lipase and inulinase, while the isolates from Aran-Bidgol playa had a great ability to produce pectinase and DNase. The strains from Urmia Lake were also good producers of DNase but failed to show any chitinase activity. The diversity of halophilic bacteria from the mentioned three saline lakes was also determined using PCR-amplified 16S rRNA followed by phylogenetic analysis of the partial 16S rRNA sequences.
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Affiliation(s)
- Hamid Babavalian
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Shirin Zahraei
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Rokhsareh Rohban
- Department of Microbiology, Faculty of Science, Science and Research Campus of Islamic Azad University, Tehran, Iran
| | - Fatemeh Shakeri
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Fernández AB, Vera-Gargallo B, Sánchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, Ventosa A. Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach. Front Microbiol 2014; 5:196. [PMID: 24847316 PMCID: PMC4021199 DOI: 10.3389/fmicb.2014.00196] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/12/2014] [Indexed: 12/02/2022] Open
Abstract
We analyzed the prokaryotic community structure of a saltern pond with 21% total salts located in Isla Cristina, Huelva, Southwest Spain, close to the Atlantic ocean coast. For this purpose, we constructed a metagenome (designated as IC21) obtained by pyrosequencing consisting of 486 Mb with an average read length of 397 bp and compared it with other metagenomic datasets obtained from ponds with 19, 33, and 37% total salts acquired from Santa Pola marine saltern, located in Alicante, East Spain, on the Mediterranean coast. Although the salinity in IC21 is closer to the pond with 19% total salts from Santa Pola saltern (designated as SS19), IC21 is more similar at higher taxonomic levels to the pond with 33% total salts from Santa Pola saltern (designated as SS33), since both are predominated by the phylum Euryarchaeota. However, there are significant differences at lower taxonomic levels where most sequences were related to the genus Halorubrum in IC21 and to Haloquadratum in SS33. Within the Bacteroidetes, the genus Psychroflexus is the most abundant in IC21 while Salinibacter dominates in SS33. Sequences related to bacteriorhodopsins and halorhodopsins correlate with the abundance of Haloquadratum in Santa Pola SS19 to SS33 and of Halorubrum in Isla Cristina IC21 dataset, respectively. Differences in composition might be attributed to local ecological conditions since IC21 showed a decrease in the number of sequences related to the synthesis of compatible solutes and in the utilization of phosphonate.
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Affiliation(s)
- Ana B Fernández
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante Alicante, Spain
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante Alicante, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
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39
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Amoozegar MA, Bagheri M, Makhdoumi-Kakhki A, Didari M, Schumann P, Nikou MM, Sánchez-Porro C, Ventosa A. Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake. Int J Syst Evol Microbiol 2014; 64:1964-1969. [PMID: 24599898 DOI: 10.1099/ijs.0.058545-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-positive, moderately halophilic bacterium, designated strain A76(T), was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells were strictly aerobic, coccus-shaped, non-motile, non-sporulating, and catalase- and oxidase-positive. Strain A76(T) grew between pH 7.0 and 10.0 (optimal growth at pH 8.0), between 20 and 45 °C (optimal growth at 35 °C) and at salinities of 0.5 to 12.5% (w/v) NaCl (optimal growth at 7.5%, w/v, NaCl). On the basis of 16S rRNA gene sequence analysis, strain A76(T) was shown to belong to the phylum Firmicutes with sequence similarities of 94.1, 93.1 and 91.1%, to the type species of the genera Jeotgalicoccus, Salinicoccus and Nosocomiicoccus, respectively. The DNA G+C content of this new isolate was 38.8 mol%. The major cellular fatty acids of strain A76(T) were anteiso-C(15 : 0) and iso-C(15 : 0), and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, an unknown lipid and two unknown phospholipids. The isoprenoid quinones were MK-6 (94%), MK-5 (3%) and MK-7 (3%). The amino acid constituents of the cell wall were Lys, Asp, Gly, Glu and Ala. The physiological, biochemical and phylogenetic differences between strain A76(T) and type strains of taxa with validly published names suggest that this strain represents a novel species in a novel genus within the family Staphylococcaceae, for which the name Aliicoccus persicus gen. nov., sp. nov. is proposed. The type strain of Aliicoccus persicus is strain A76(T) ( = CECT 8508(T) = DSM 28306(T) = IBRC-M 10081(T)).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Bagheri
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maryam Didari
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | | | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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40
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Baricz A, Coman C, Andrei AS, Muntean V, Keresztes ZG, Păuşan M, Alexe M, Banciu HL. Spatial and temporal distribution of archaeal diversity in meromictic, hypersaline Ocnei Lake (Transylvanian Basin, Romania). Extremophiles 2014; 18:399-413. [PMID: 24414798 DOI: 10.1007/s00792-013-0625-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/29/2013] [Indexed: 12/31/2022]
Abstract
Saline, meromictic lakes with significant depth are usually formed as a result of salt mining activity. Ocnei Lake is one of the largest Transylvanian (Central Romania) neutral, hypersaline lake of man-made origin. We aimed to survey the seasonal dynamics of archaeal diversity in the water column of Ocnei Lake by employing microbiological methods as well as molecular techniques based on the sequence analysis of the 16S rRNA gene. We found that archaeal diversity in the water column increased with depth and salinity, with 8 OTUs being detected in the epilimnion compared to 21 found in the chemocline, and 32 OTUs in the monimolimnion. Down to 3.5 m depth, the archaeal community was markedly dominated by the presence of an unclassified archaeon sharing 93% sequence identity to Halogeometricum spp. At the chemocline, the shift in archaeal community composition was associated with an increase in salinity, the main factor affecting the vertical distribution of archaeal assemblages. It appears that the microoxic and hypersaline monimolimnion is populated by several major haloarchaeal taxa, with minor fluctuations in their relative abundances throughout all seasons. The culturable diversity was reasonably correlated to the dominant OTUs obtained by molecular methods. Our results indicate that Ocnei Lake represents a relatively stable extreme habitat, accommodating a diverse and putatively novel archaeal community, as 30% of OTUs could not be classified at the genus level.
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Affiliation(s)
- Andreea Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 5-7 Clinicilor Street, 400006, Cluj-Napoca, Romania
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41
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Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME JOURNAL 2013; 8:979-90. [PMID: 24335829 DOI: 10.1038/ismej.2013.221] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/05/2013] [Accepted: 11/10/2013] [Indexed: 02/01/2023]
Abstract
Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate, but not sodium, chloride or calcium ions, while relative abundances of Halorubrum, Haloarcula, Halonotius, Halobaculum and Salinibacter-related sequences correlated negatively with Haloquadratum and these same ionic factors. Nanohaloarchaea and Halorhabdus-related sequence abundances were inversely correlated with each other, but not other taxonomic groups. These data, along with predicted gene functions from nearly-complete assembled population metagenomes, suggest different ecological phenotypes for Nanohaloarchaea and Halorhabdus-related strains versus other community members. Nucleotide percent G+C compositions were consistently lower in community metagenomic reads from summer versus winter samples. The same seasonal G+C trends were observed within taxonomically binned read subsets from each of seven different genus-level archaeal groups. Relative seasonal abundances were also linked to percent G+C for assembled population genomes. Together, these data suggest that extreme ionic conditions may exert selective pressure on archaeal populations at the level of genomic nucleotide composition, thus contributing to seasonal successional processes. Despite the unavailability of cultured representatives for most of the organisms identified in this study, effective coordination of physical and biological measurements has enabled discovery and quantification of unexpected taxon-specific, environmentally mediated factors influencing microbial community structure.
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42
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Amoozegar MA, Didari M, Bagheri M, Fazeli SAS, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Bacillus
salsus sp. nov., a halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63:3324-3329. [DOI: 10.1099/ijs.0.050120-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, endospore-forming, rod-shaped, strictly aerobic, slightly halophilic bacterium, designated strain A24T, was isolated from the hypersaline lake Aran-Bidgol in Iran. Cells of strain A24T were motile rods and produced oval endospores at a terminal position in swollen sporangia. Strain A24T was catalase and oxidase positive. Growth occurred with between 0.5 and 7.5 % (w/v) NaCl and the isolate grew optimally at 3 % (v/w) NaCl. The optimum temperature and pH for growth were 35 °C and pH 8.0, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A24T belonged to the genus
Bacillus
within the phylum
Firmicutes
and showed the closest phylogenetic similarity with the species
Bacillus alkalitelluris
BA288T (97.2 %),
Bacillus herbersteinensis
D-1,5aT (96.0 %) and
Bacillus litoralis
SW-211T (95.6 %). The G+C content of the genomic DNA of this strain was 35.9 mol%. The polar lipid pattern of strain A24T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids of strain A24T were anteiso-C15 : 0 and iso-C15 : 0. The respiratory quinones were MK-7 (94 %) and MK-6 (4 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate A24T within the genus
Bacillus
. DNA–DNA hybridization experiments revealed a relatedness of 8 % between strain A24T and
Bacillus alkalitelluris
IBRC-M 10596T, supporting its placement as a novel species. Phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data suggest that this strain represents a novel species of the genus
Bacillus
, for which the name
Bacillus
salsus sp. nov. is proposed. The type strain is strain A24T ( = IBRC-M 10078 T = KCTC 13816T).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Didari
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Bagheri
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | | | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Amoozegar MA, Makhdoumi-Kakhki A, Mehrshad M, Fazeli SAS, Ventosa A. Halopenitus
malekzadehii sp. nov., an extremely halophilic archaeon isolated from a salt lake. Int J Syst Evol Microbiol 2013; 63:3232-3236. [DOI: 10.1099/ijs.0.050500-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain CC65T, a novel extremely halophilic archaeon, was isolated from a brine sample of a salt lake in Iran. The novel strain was light yellow-pigmented, non-motile, pleomorphic and required at least 1.7 M NaCl and 0.02 M MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.4 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C, respectively, while it was able to grow over a pH and a temperature range of pH 6.5–9.0 and 30–50 °C, respectively. Analysis of 16S rRNA gene sequence revealed that strain CC65T clustered with the sole member of the genus
Halopenitus
,
Halopenitus persicus
DC30T with a sequence similarity of 98.0 %. The polar lipid profile of strain CC65T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. An unidentified glycolipid and two minor phospholipids were also observed. The only quinone present was MK-8(II-H2). The DNA G+C content of strain CC65T was 63.8 mol%. On the basis of the biochemical and physiological characteristics, as well as DNA–DNA hybridization (44 % with
Halopenitus persicus
IBRC 10041T), strain CC65T is classified as a novel species of the genus
Halopenitus
, for which the name
Halopenitus
malekzadehii sp. nov. is proposed. The type strain is CC65T ( = IBRC-M 10418T = KCTC 4045T).
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Affiliation(s)
- Mohammad Ali Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Ali Makhdoumi-Kakhki
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maliheh Mehrshad
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR Tehran, Iran
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | | | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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44
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Casamayor EO, Triadó-Margarit X, Castañeda C. Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain. FEMS Microbiol Ecol 2013; 85:503-18. [DOI: 10.1111/1574-6941.12139] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Emilio O. Casamayor
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
| | - Xavier Triadó-Margarit
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
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45
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Marinobacter persicus sp. nov., a moderately halophilic bacterium from a saline lake in Iran. Antonie van Leeuwenhoek 2013; 104:47-54. [DOI: 10.1007/s10482-013-9923-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/09/2013] [Indexed: 11/25/2022]
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46
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Bacillus
persicus sp. nov., a halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63:1229-1234. [DOI: 10.1099/ijs.0.042689-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-positive, slightly halophilic bacterium, designated strain B48T, was isolated from soil around the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain B48T were non-motile rods and produced ellipsoidal endospores at a central or subterminal position in swollen sporangia. Strain B48T was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5–10.0 % (w/v), with optimum growth occurring at 2.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.5–8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain B48T was shown to belong to the genus
Bacillus
within the phylum
Firmicutes
and showed the closest phylogenetic similarity to the species
Bacillus foraminis
CV53T (97.4 %) and
Bacillus purgationiresistens
DS22T (96.9 %). The DNA G+C content of this new isolate was 40.1 mol%. The major cellular fatty acids of strain B48T were iso-C15 : 0 and anteiso-C15 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid and two unknown phospholipids. The only quinone present was menaquinone 7 (MK-7). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate B48T within the genus
Bacillus
. DNA–DNA hybridization experiments revealed a low level of relatedness between strain B48T and
Bacillus foraminis
IBRC-M 10625T (8.1 %). On the basis of polyphasic evidence from this study, a new species of the genus
Bacillus
,
Bacillus
persicus sp. nov., is proposed, with strain B48T ( = IBRC-M 10115T = DSM 25386T = CECT 8001T) as the type strain.
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47
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Mehrshad M, Amoozegar MA, Didari M, Bagheri M, Fazeli SAS, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Bacillus halosaccharovorans sp. nov., a moderately halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63:2776-2781. [PMID: 23291894 DOI: 10.1099/ijs.0.046961-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, moderately halophilic bacterium, designated strain E33(T), was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells of strain E33(T) were motile rods and produced ellipsoidal endospores at a central or subterminal position in swollen sporangia. Strain E33(T) was a strictly aerobic bacterium, catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-25 % (w/v), with optimum growth occurring at 5-15 % (w/v) NaCl. The optimum temperature and pH for growth were 40 °C and pH 7.5-8.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain E33(T) was shown to belong to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity with the species Bacillus niabensis 4T19(T) (99.2 %), Bacillus herbersteinensis D-1-5a(T) (97.3 %) and Bacillus litoralis SW-211(T) (97.2 %). The DNA G+C content of the type strain of the novel species was 42.6 mol%. The major cellular fatty acids of strain E33(T) were anteiso-C15 : 0 and iso-C15 : 0, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids, an unknown lipid and an unknown phospholipid. The isoprenoid quinones were MK-7 (97 %), MK-6 (2 %) and MK-8 (0.5 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features confirm the placement of isolate E33(T) within the genus Bacillus. DNA-DNA hybridization experiments revealed low levels of relatedness between strain E33(T) and Bacillus niabensis IBRC-M 10590(T) (22 %), Bacillus herbersteinensis CCM 7228(T) (38 %) and Bacillus litoralis DSM 16303(T) (19 %). On the basis of polyphasic evidence from this study, a novel species of the genus Bacillus, Bacillus halosaccharovorans sp. nov. is proposed, with strain E33(T) (= IBRC-M 10095(T) = DSM 25387(T)) as the type strain.
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Affiliation(s)
- Maliheh Mehrshad
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of living organisms, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of living organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Didari
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of living organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Bagheri
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran.,Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of living organisms, College of Science, University of Tehran, Tehran, Iran
| | - Seyed Abolhassan Shahzadeh Fazeli
- Department of Genetics, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Peter Schumann
- DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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48
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Shafiei M, Ziaee AA, Amoozegar MA. Purification and characterization of a halophilic α-amylase with increased activity in the presence of organic solvents from the moderately halophilic Nesterenkonia sp. strain F. Extremophiles 2012; 16:627-35. [PMID: 22592324 DOI: 10.1007/s00792-012-0462-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
Abstract
An extracellular halophilic α-amylase was purified from Nesterenkonia sp. strain F using 80 % ethanol precipitation and Q-Sepharose anion exchange chromatography. The enzyme showed a single band with an apparent molecular weight of 110 kDa by SDS-PAGE. The amylase exhibited maximal activity at pH 7-7.5, being relatively stable at pH 6.5-7.5. Optimal temperature for the amylase activity and stability was 45 °C. The purified enzyme was highly active in the broad range of NaCl concentrations (0-4 M) with optimal activity at 0.25 M NaCl. The amylase was highly stable in the presence of 3-4 M NaCl. Amylase activity was not influenced by Ca²⁺, Rb⁺, Li⁺, Cs⁺, Mg²⁺ and Hg²⁺, whereas Fe³⁺, Cu²⁺, Zn²⁺ and Al³⁺) strongly inhibited the enzyme activity. The α-amylase was inhibited by EDTA, but was not inhibited by PMSF and β-mercaptoethanol. K(m) value of the amylase for soluble starch was 6.6 mg/ml. Amylolytic activity of the enzyme was enhanced not only by 20 % of water-immiscible organic solvents but also by acetone, ethanol and chloroform. Higher concentration (50 %) of the water-miscible organic solvents had no significant effect on the amylase activity. To the best of our knowledge, this is the first report on increased activity of a microbial α-amylase in the presence of organic solvents.
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Affiliation(s)
- Mohammad Shafiei
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, P. O. Box 65355141, Ahvaz, Iran.
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