Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt

Echigo, Akinobu; Minegishi, Hiroaki; Shimane, Yasuhiro; Kamekura, Masahiro; Itoh, Takashi; Usami, Ron

doi:10.1099/ijs.0.049965-0

Cited by 38 publications

(22 citation statements)

References 28 publications

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“…The description of this family, the type genus of which is Halobacterium (Elazari-Volcani, 1957; Skerman et al , 1980; Larsen & Grant, 1989), is the same as that of the order Halobacteriales . The genera that are presently part of this family are Haladaptatus (Savage et al , 2007), Halalkalicoccus (Xue et al , 2005), Halapricum (Song et al , 2014), Haloarchaeobius (Makhdoumi-Kakhki et al , 2012a), Halarchaeum (Minegishi et al , 2010b), Haloarcula (Torreblanca et al , 1986), Halobacterium (Elazari-Volcani, 1957; Skerman et al , 1980), Halococcus (Schoop, 1935; Skerman et al , 1980), Halomarina (Inoue et al , 2011), Halomicroarcula (Echigo et al , 2013), Halomicrobium (Oren et al , 2002), Halorientalis (Cui et al , 2011c), Halorhabdus (Wainø et al , 2000), Halorubellus (Cui et al , 2012), Halorussus (Cui et al , 2010a), Halosimplex (Vreeland et al , 2002), Halovenus (Makhdoumi-Kakhki et al , 2012b), Natronoarchaeum (Shimane et al , 2010), Natronomonas (Kamekura et al , 1997), Salarchaeum (Shimane et al , 2011…”

Section: Discussionmentioning

confidence: 97%

Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov.

Gupta

Naushad

Baker

2015

International Journal of Systematic and Evolutionary Microbiology

263

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Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. The Halobacteria constitute one of the largest groups within the Archaea. The hierarchical relationship among members of this large class, which comprises a single order and a single family, has proven difficult to determine based upon 16S rRNA gene trees and morphological and physiological characteristics. This work reports detailed phylogenetic and comparative genomic studies on .100 halobacterial (haloarchaeal) genomes containing representatives from 30 genera to investigate their evolutionary relationships. In phylogenetic trees reconstructed on the basis of 32 conserved proteins, using both neighbour-joining and maximum-likelihood methods, two major clades (clades A and B) encompassing nearly two-thirds of the sequenced haloarchaeal species were strongly supported. Clades grouping the same species/genera were also supported by the 16S rRNA gene trees and trees for several individual highly conserved proteins (RpoC, EF-Tu, UvrD, GyrA, EF-2/EF-G). In parallel, our comparative analyses of protein sequences from haloarchaeal genomes have identified numerous discrete molecular markers in the form of conserved signature indels (CSI) in protein sequences and conserved signature proteins (CSPs) that are found uniquely in specific groups of haloarchaea. Thirteen CSIs in proteins involved in diverse functions and 68 CSPs that are uniquely present in all or most genome-sequenced haloarchaea provide novel molecular means for distinguishing members of the class Halobacteria from all other prokaryotes. The members of clade A are distinguished from all other haloarchaea by the unique shared presence of two CSIs in the ribose operon protein and small GTP-binding protein and eight CSPs that are found specifically in members of this clade. Likewise, four CSIs in different proteins and five other CSPs are present uniquely in members of clade B and distinguish them from all other haloarchaea. Based upon their specific clustering in phylogenetic trees for different gene/protein sequences and the unique shared presence of large numbers of molecular signatures, members of clades A and B are indicated to be distinct from all other haloarchaea because of their uniquely shared evolutionary histories. Based upon these results, it is proposed that clades A and B be recognized as two new orders, Natrialbales ord. nov. and Haloferacales ord. nov., within the class Halobacteria, containing the novel families Natrialbaceae fam. nov. and Haloferacaceae fam. nov. Other members of the class Halobacteria that are not members of these two orders will remain part of the emended order Halobacteriales in an emended family Halobacteriaceae. INTRODUCTIONThe class Halobacteria, members of which will be referred t...

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Section: Discussionmentioning

confidence: 97%

Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov.

Gupta

Naushad

Baker

2015

International Journal of Systematic and Evolutionary Microbiology

263

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“…The genus Halomicroarcula is a member of the family Halobacteriaceae , and was first proposed by Echigo et al (2013) to accommodate the species Halomicroarcula pellucida , which is a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from a solar salt sample imported from France. Recently, Halomicroarcula limicola was described, based on a strain isolated from a marine solar saltern (Zhang & Cui, 2014).…”

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confidence: 99%

Halomicroarcula salina sp. nov., isolated from a marine solar saltern

Zhang

Cui

2015

International Journal of Systematic and Evolutionary Microbiology

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Halophilic archaeal strain YGHS18 T was isolated from the Yinggehai marine solar saltern near Shanya city of Hainan Province, China. Cells from the strain were observed to be pleomorphic rods, stained Gram-negative, and formed red-pigmented colonies on solid media. Strain YGHS18 T was found to be able to grow at 20-50 6C (optimum 37 6C), with 0.9-4.8 M NaCl (optimum 2.1 M) and at pH 5.5-9.0 (optimum pH 7.0). The cells lysed in distilled water and the minimum NaCl concentration to prevent cell lysis was found to be 0.9 M. The major polar lipids of the strain were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, glucosyl mannosyl glucosyl diether and a diglycosyl diether (DGD-2). Strain YGHS18 T possessed two heterogeneous 16S rRNA genes (rrnA and rrnB) and both were related to those of members of the genera Haloarcula (93.1-96.9 % sequence similarity) and Halomicroarcula (92.7-96.1 % similarity). The rrnA gene (orthologous gene) of strain YGHS18 T clustered phylogenetically with members of the genus Halomicroarcula while the rrnB gene formed a paraphyly with members of the genera Halomicroarcula and Haloarcula. The rpoB9 gene of strain YGHS18 T was related phylogenetically to species of the genera Halomicroarcula (91.6-92.7 % sequence similarity) and Haloarcula (91.5-92.4 % similarity). EF-2 gene analysis revealed that strain YGHS18 T was related phylogenetically to species of the genus Halomicroarcula (92.2-92.9 % sequence similarity) rather than to those of the genus Haloarcula (90.9-91.7 % similarity). The DNA G+C content of strain YGHS18 T was determined to be 64.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YGHS18 T (5CGMCC 1.12128 T 5JCM 18369 T) represents a novel species of the genus Halomicroarcula, for which the name Halomicroarcula salina sp. nov. is proposed.

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“…Halomicroarcula pellucida (isolated from solar salt, France) [64] is the type species of the genus Halomicroarcula. It grows optimally at 4.3 M NaCl, pH 7 and 40 C. Hma.…”

Section: Order Halobacterialesmentioning

confidence: 99%

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes

et al. 2017

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Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications. SYSTEMATICS OF HALOPHILIC ARCHAEAHalophilic micro-organisms are found in the three domains of life, and are extremophiles living in hypersaline environments in the presence of salt (generally NaCl) as a specific requisite for their growth [1]. Hypersaline environments contain higher salt concentrations than seawater (3.5 % total dissolved salts) [2]. According to the optimum NaCl concentration for growth, micro-organisms fall into one of the following categories: extreme halophiles with optimum growth at 15-30 % (2.5-5.2 M) NaCl; moderate halophiles with optimum growth at 3-15 % (0.5-2.5 M) NaCl; slight halophiles with optimum growth at 1-3 % (0.2-0.5 M) NaCl; non-halophiles with optimum growth at less than 1 % (0.2 M) NaCl; and halotolerant micro-organisms which are non-halophiles showing the ability to tolerate high NaCl concentrations [3]. Halophiles can live in hypersaline environments because they are able to sustain osmotic balance. They use two main strategies to withstand the adverse consequences of water loss when exposed to high salt concentrations. The first strategy used by extremely halophilic archaea (haloarchaea) and halophilic anaerobic bacteria such as members of Halanaerobiales is known as the 'salt-in-cytoplasm' strategy, during which salts such as NaCl or KCl accumulate in the cytoplasm at concentrations similar to the extracellular ones [4,5]. Another mechanism to cope with high salt concentrations is the accumulation of organic molecules such as amino acids, sugars and polyols, known as compatible solutes or osmolytes. Compatible solutes are small and highly soluble molecules that can...

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Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt

Cited by 38 publications

References 28 publications

Halomicroarcula salina sp. nov., isolated from a marine solar saltern

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes

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