Genome-based taxonomy of genera Haloarcula and Halomicroarcula, and description of six novel species of Haloarcula

The genera Haloarcula and Halomicroarcula are the most closely related genera within the family Haloarculaceae (class Halobacteria). The respective 16S rRNA genes of type strains from the genus Haloarcula showed 94.7-96.5% similarities to their homologous genes of type strains from the genus Halomicroarcula. The Haloarcula species showed 89.3-92.8% rpoB' gene similarities to Halomicroarcula species. These similarities were higher than the proposed genus boundary. Phylogenomic analysis revealed that these two genera formed a tight cluster separated from Halomicrobium with high bootstrap confidence. The average amino acid identity (AAI) values among Haloarcula and Halomicroarcula were 70.1-74.5%, higher than the cutoff value (67.0%) to differentiate the genera Haloarcula and Halomicroarcula from Halomicrobium. These results indicated that the genus Halomicroarcula should be merged with Haloarcula. Then, six novel species are described based on strains DFY41T, GDY20T, SHR3T, XH51T, YJ-61-ST, and ZS-22-S1T isolated from coarse sea salt, marine solar saltern, and salt lake (China). These six strains formed separate clades (90.1-99.3% 16S rRNA and 89.0-94.9% rpoB' gene similarities) and then clustered with current Haloarcula and Halomicroarcula species (89.4-99.1% 16S rRNA and 87.6-95.0% rpoB' gene similarities), as revealed by phylogenetic analyses. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and AAI values among these six strains and current Haloarcula and Halomicroarcula species were 76.2-89.8%, 25.3-46.0%, and 70.3-89.7%, respectively, clearly below the species demarcation threshold. These six strains were distinguished from current Haloarcula and Halomicroarcula species according to differential phenotypic characteristics. Six novel species, Haloarcula halophila sp. nov., Haloarcula litorea sp. nov., Haloarcula rara sp. nov., Haloarcula halobia sp. nov., Haloarcula pelagica sp. nov., and Haloarcula ordinaria sp. nov., are proposed to accommodate strains DFY41T, GDY20T, SHR3T, XH51T, YJ-61-ST, and ZS-22-S1T, respectively.

Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach

An extremely halophilic archaeon, strain S1AR25-5AT, was isolated from a hypersaline soil sampled in Odiel Saltmarshes Natural Area (Huelva, Spain). The cells were Gram-stain-negative, motile, pleomorphic rods. Cell growth was observed in the presence of 15-30 % (w/v) NaCl [optimum, 25 % (w/v) NaCl], at pH 6.0-9.0 (optimum, pH 6.5-7.5) and at 25-50 °C (optimum, 37 °C). Based on the 16S rRNA and rpoB' gene sequence comparisons, strain S1AR25-5AT was affiliated to the genus Haloarcula. Taxogenomic analysis, including comparison of the genomes and the phylogenomic tree based on the core-orthologous proteins, together with the genomic indices, i.e., orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, confirmed that strain S1AR25-5AT (=CCM 9249T=CECT 30619T) represents a new species of the genus Haloarcula, for which we propose the name Haloarcula terrestris sp. nov. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and an unidentified glycolipid, which correlated with the lipid profile of species of the genus Haloarcula. In addition, based on the modern approach in description of species in taxonomy of prokaryotes, the above mentioned genomic indexes indicated that the species Haloarcula tradensis should be considered as a heterotypic synonym of Haloarcula argentinensis.

Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico

The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.

Comparative diversity analysis of halophiles at two polar saltern systems in Indramayu, West Java, Indonesia

Successive microbes in solar salt ponds are essential since it is well correlated with the quality of salt produced. This research aimed to analyse the microbial diversity of the solar salt ponds in Indonesia, which use high-density polyethylene in the ponds. There are two systems, that is, an integrated open system (In-system) and a closed system (Tt-system). The In-system uses seawater while the Tt-system uses seawater from the saline artesian well. Results showed that the In-system had richer microbes than the Tt-system. Both systems shared similar halophilic microbes profile. Ponds with low salinity (3-4 Be) had very low archaea, that is, 0·2 and 0·7% for the In-system and Tt-system respectively and were dominantly inhabited by phylum Proteobacteria. In the pond with high salinity, that is, 25 Be, both systems were dominated by the phylum Euryarchaeota, family Halobacteriaceae, and genera Halorubrum was dominantly found in In25 ponds and Tt25 ponds. Even though the two systems use the same parent seawater, that is, the Java Sea and share similar microbial composition at the phylum level, we found the dominance identified microbes in both systems were different.

Haloarcula mannanilytica sp. nov., a galactomannan-degrading haloarchaeon isolated from commercial salt

A mannan-degrading halophilic archaeal strain, MD130-1^T, was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented. Strain MD130-1^T was able to grow at 1.5-4.6 M NaCl (optimum, 3.6 M) at pH 6.0-8.0 (optimum, pH 7.0) and at 25-50 °C (optimum, 40 °C). The DNA G+C content was 62.1 mol% (genome). The orthologous 16S rRNA gene sequence showed the highest similarity (99.4 %) to those of Haloarcula japonica JCM 7785^T and Haloarcula hispanica JCM 8911^T. The values of genome relatedness between strain MD130-1^T and Haloarcula species were 84.33-85.96 % in ANIb and 30.4-32.9 % using GGDC formula 2. The polar lipids of strain MD130-1^T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and triglycosyl diether-2. Based on the results of phenotypic and phylogenetic analyses, the strain represents a new species of the genus Haloarcula, for which the name Haloarcula mannanilytica sp. nov. is proposed. The type strain is MD130-1^T (=JCM 33835^T=KCTC 4287^T) isolated from commercial salt made in Ishikawa prefecture, Japan.