Proposed minimal standards for description of new taxa of the class Halobacteria

Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB' gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.

4-O-Glucosylation of Trichothecenes by Fusarium Species: A Phase II Xenobiotic Metabolism for t-Type Trichothecene Producers

The t-type trichothecene producers Fusarium sporotrichioides and Fusarium graminearum protect themselves against their own mycotoxins by acetylating the C-3 hydroxy group with Tri101p acetylase. To understand the mechanism by which they deal with exogenously added d-type trichothecenes, the Δtri5 mutants expressing all but the first trichothecene pathway enzymes were fed with trichodermol (TDmol), trichothecolone (TCC), 8-deoxytrichothecin, and trichothecin. LC-MS/MS and NMR analyses showed that these C-3 unoxygenated trichothecenes were conjugated with glucose at C-4 by α-glucosidic linkage. As t-type trichothecenes are readily incorporated into the biosynthetic pathway following the C-3 acetylation, the mycotoxins were fed to the ΔFgtri5ΔFgtri101 mutant to examine their fate. LC-MS/MS and NMR analyses demonstrated that the mutant conjugated glucose at C-4 of HT-2 toxin (HT-2) by α-glucosidic linkage, while the ΔFgtri5 mutant metabolized HT-2 to 3-acetyl HT-2 toxin and T-2 toxin. The 4-O-glucosylation of exogenously added t-type trichothecenes appears to be a general response of the ΔFgtri5ΔFgtri101 mutant, as nivalenol and its acetylated derivatives appeared to be conjugated with hexose to some extent. The toxicities of 4-O-glucosides of TDmol, TCC, and HT-2 were much weaker than their corresponding aglycons, suggesting that 4-O-glucosylation serves as a phase II xenobiotic metabolism for t-type trichothecene producers.

Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena

The haloarchaeal genera Natrinema and Haloterrigena were described almost simultaneously by two different research groups and some strains studied separately were described as different species of these genera. Furthermore, the description of additional species were assigned to either Natrinema or Haloterrigena, mainly on the basis of the phylogenetic comparative analysis of single genes (16S rRNA gene and more recently rpoB’ gene), but these species were not adequately separated or assigned to the corresponding genus. Some studies suggested that the species of these two genera should be unified into a single genus, while other studies indicated that the genera should remain but some of the species should be reassigned. In this study, we have sequenced or collected the genomes of the type strains of species of Natrinema and Haloterrigena and we have carried out a comparative genomic analysis in order to clarify the controversy related to these two genera. The phylogenomic analysis based on the comparison of 525 translated single-copy orthologous genes and the Overall Genome Relatedness Indexes (i.e., AAI, POCP, ANI, and dDDH) clearly indicate that the species Haloterrigena hispanica, Haloterrigena limicola, Haloterrigena longa, Haloterrigena mahii, Haloterrigena saccharevitans, Haloterrigena thermotolerans, and Halopiger salifodinae should be transferred to the genus Natrinema, as Natrinema hispanicum, Natrinema limicola, Natrinema longum, Natrinema mahii, Natrinema saccharevitans, Natrinema thermotolerans, and Natrinema salifodinae, respectively. On the contrary, the species Haloterrigena turkmenica, Haloterrigena salifodinae, and Haloterrigena salina will remain as the only representative species of the genus Haloterrigena. Besides, the species Haloterrigena daqingensis should be reclassified as a member of the genus Natronorubrum, as Natronorubrum daqingense. At the species level, Haloterrigena jeotgali and Natrinema ejinorense should be considered as a later heterotypic synonyms of the species Haloterrigena (Natrinema) thermotolerans and Haloterrigena (Natrinema) longa, respectively. Synteny analysis and phenotypic features also supported those proposals.

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.

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra- and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.

Natronoarchaeum persicum sp. nov., a haloarchaeon isolated from a hypersaline lake

A novel halophilic archaeon, designated strain WIIAL99T, was isolated from Lake Meyghan, a hypersaline lake in Iran. Cells of strain WIIAL99T were non-motile, catalase-positive and oxidase-negative. Strain WIIAL99T required at least 2.5 M NaCl and 0.05 M MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 37-40 °C; it was able to grow at pH 6.0-8.5 and 20-55 °C. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of strain WIIAL99T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, disulfated diglycosyl diether and one unidentified glycolipid. The DNA G+C content of strain WIIAL99T was 66.7 mol%. The closest relative was Natronoarchaeum rubrum JCM 17119T with 98.2 % similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB' gene sequences indicated that strain WIIAL99T is a member of the genus Natronoarchaeum in the family Halobacteriaceae and forms a distinct cluster. It was concluded that strain WIIAL99T (=IBRC-M 11062T=LMG 29814T) represents a novel species of the genus Natronoarchaeum, for which the name Natronoarchaeum persicum sp. nov. is proposed.

Natrinema soli sp. nov., a novel halophilic archaeon isolated from a hypersaline wetland

An extremely halophilic archaeon, designated strain 5-3T, was isolated from a soil sample of Meighan wetland in Iran. Strain 5-3T was strictly aerobic, catalase-positive and oxidase-negative. Cells were Gram-stain-negative, non-motile and ovoid. Colonies of strain 5-3T were cream-coloured. The isolate showed optimum growth at 4.0 M NaCl, 40 °C and pH 7.0. The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two unknown phospholipids and three glycolipids (including one that was chromatographically identical to S2-DGD). The major respiratory quinone was menaquinone MK-8. The G+C content of the genomic DNA was 61.5 mol%. The closest relative was Natrinema salaciae JCM 17869T with 97.3 % similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB' gene sequences indicated that strain 5-3T is a member of the genus Natrinema in the family Natrialbaceae and forms a distinct cluster. On the basis of phylogenetic analysis, and phenotypic and chemotaxonomic characteristics, a novel species of the family Natrialbaceae, Natrinema soli sp. nov., is proposed. The type strain is 5-3T (=IBRC-M 11063T=LMG 29247T).

Haloparvum alkalitolerans sp. nov., alkali-tolerant haloarchaeon isolated from commercial salt

A Gram-stain-negative, rod-pleomorphic, aerobic, halophilic archaeon, strain MK62-1T, was isolated from commercial salt made from seawater in the Philippines. Strain MK62-1T was able to grow at 2.1-4.7 M NaCl (with optimum at 2.1-2.6 M NaCl), pH 6.5-9.5 (optimum, pH 7.0-7.5) and 20-55 °C (optimum, 45-50 °C). Based on the orthologous 16S rRNA gene sequence, the closest relative was Haloparvum sedimenti JCM 30891T with 99.2 % similarity. The RNA polymerase subunit B' gene sequence also showed the highest similarity (97.4 %) to that of Haloparvum sedimenti DYS4T. The DNA G+C content of MK62-1T was 70.1 mol%, while that of Haloparvum sedimenti JCM 30891T was 69.5 mol% by the HPLC method. The levels of DNA-DNA relatedness between MK62-1T and Haloparvum sedimenti JCM 30891T were 60.6 and 60.8 % (reciprocally). The major polar lipids of the isolate were C20C20 archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Based on the phenotypic and phylogenetic analyses, it is proposed that the isolate represents species within the genus Haloparvum, for which the name Haloparvum alkalitolerans sp. nov. is proposed. The type strain is MK62-1T (=JCM 30442T =KCTC 4214T).

Halopiger thermotolerans sp. nov., a thermo-tolerant haloarchaeon isolated from commercial salt

Three thermo-tolerant halophilic archaeal strains, SR-441T, SR-412 and SR-188, were isolated from commercial salt samples. Cells were non-motile pleomorphic rod-shaped, and stained Gram-negative. Colonies were pink-pigmented. The three strains were able to grow with 1.7-4.6 M NaCl (optimum, 2.5 M), at pH 6.5-9.0 (optimum, pH 8.0) and at 35-60 °C (optimum, 45 °C). The orthologous 16S rRNA gene sequence similarities amongst the three strains were 98.8-99.3 %, and the level of DNA-DNA relatedness was 71-74 and 72-75 % (reciprocally). The closest relative was Halopiger aswanensis JCM 11628T with 98.6 %-99.1 % similarity in the orthologous 16S rRNA gene sequences, followed by two more Halopiger species, Halopiger xanaduensis JCM 14033T (98.5 %-99.1 %) and Halopiger salifodinae JCM 9578T (95.5 %-95.6 %). DNA-DNA relatednesses between the three strains and H. aswanensis JCM 11628T and H. xanaduensis JCM 14033T were 61 and 54 %, respectively. The polar lipids of the three novel strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and bis-sulfated diglycosyl archaeol-1. The most distinctive feature of the three strains was the ability to grow at 60 °C, while the maximum growth temperature of H. aswanensis is 55 °C. Based on phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halopiger, for which the name Halopiger thermotolerans sp. nov. is proposed. The type strain is SR-441T (=JCM 19583T=KCTC 4248T) isolated from solar salt produced in Australia. SR-412 (=JCM 19582) and SR-188 (=JCM 19581) isolated from commercial salt samples are additional strains of the species.

Halarchaeum grantii sp. nov., a moderately acidophilic haloarchaeon isolated from a commercial salt sample

Three moderately acidophilic, halophilic archaeal strains, MH1-243-3T, MH1-243-5 and MH1-243-6, were isolated from a commercial salt sample made from seawater in Okinawa, Japan. Cells of the three strains were pleomorphic and stained Gram-negative. Colonies of the strains were orange-red-pigmented. Strain MH1-243-3T was able to grow at 15-27 % (w/v) NaCl (optimum 24 °C), at pH 4.5-6.5 (pH 5.5) and at 35-50 °C (45 °C). Strains MH1-243-5 and MH1-243-6 grew within slightly different ranges (shown in text). The 16S rRNA gene sequences of the three strains were identical, and the closest phylogenetic relative was Halarchaeum salinum MH1-34-1T with 97.0 % similarity. The rpoB' gene sequences of the three strains were also identical, and the closest phylogenetic relative was Halarchaeum acidiphilum JCM 16109T with 92.0 % similarity. The DNA G+C content of MH1-243-3T, MH1-243-5 and MH1-243-6 was 65.2 mol%. The levels of DNA-DNA relatedness amongst the three strains were 84.1-99.8 %, while that between MH1-243-3T and H. salinum MH1-34-1T was 30.6 % and 31.6 % (reciprocally), and those between MH1-243-3T and type strains of other species in the genus Halarchaeum were 42.3-29.4 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum, for which the name Halarchaeum grantii sp. nov. is proposed. The type strain is MH1-243-3T ( = JCM 19585T = KCTC 4142T), isolated from commercial sea salt produced in Okinawa, Japan. MH1-243-5 ( = JCM 19586) and MH1-243-6 ( = JCM 18422) are additional strains of the species.

Halorubrum gandharaense sp. nov., an alkaliphilic haloarchaeon from commercial rock salt

A Gram-stain-negative, non-motile, pleomorphic rod-shaped, orange–red-pigmented, facultatively aerobic and haloalkaliphilic archaeon, strain MK13-1T, was isolated from commercial rock salt imported from Pakistan. The NaCl, pH and temperature ranges for growth of strain MK13-1T were 3.0–5.2 M NaCl, pH 8.0–11.0 and 15–50 °C, respectively. Optimal growth occurred at 3.2–3.4 M NaCl, pH 9.0–9.5 and 45 °C. Addition of Mg2+ was not required for growth. The major polar lipids of the isolate were C20C20 and C20C25 archaeol derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Glycolipids were not detected. The DNA G+C content was 64.1 mol%. The 16S rRNA gene sequence of strain MK13-1T was most closely related to those of the species of the genus Halorubrum, Halorubrum luteum CECT 7303T (95.9 % similarity), Halorubrum alkaliphilum JCM 12358T (95.3 %), Halorubrum kocurii JCM 14978T (95.3 %) and Halorubrum lipolyticum JCM 13559T (95.3 %). The rpoB′ gene sequence of strain MK13-1T had < 90 % sequence similarity to those of other members of the genus Halorubrum. Based on the phylogenetic analysis and phenotypic characterization, strain MK13-1T may represent a novel species of the genus Halorubrum, for which the name Halorubrum gandharaense sp. nov. is proposed, with the type strain MK13-1T ( = JCM 17823T = CECT 7963T).

Halococcus agarilyticus sp. nov., an agar-degrading haloarchaeon isolated from commercial salt

Two agar-degrading halophilic archaeal strains, 62ET and 197A, were isolated from commercial salt samples. Cells were non-motile cocci, approximately 1.2–2.0 µm in diameter and stained Gram-negative. Colonies were pink-pigmented. Strain 62ET was able to grow with 24–30 % (w/v) NaCl (optimum, 27 %), at pH 6.5–8.5 (optimum, pH 7.5) and at 22–47 °C (optimum, 42 °C). The 16S rRNA gene sequences of strains 62ET and 197A were identical, and the level of DNA–DNA relatedness between them was 90 and 90 % (reciprocally). The closest relative was Halococcus saccharolyticus JCM 8878T with 99.7 % similarity in 16S rRNA orthologous gene sequences, followed by Halococcus salifodinae JCM 9578T (99.6 %), while similarities with other species of the genus Halococcus were equal to or lower than 95.1 %. The rpoB′ gene tree strongly supported that the two strains were members of the genus Halococcus . Mean DNA–DNA relatedness between strain 62ET and H. saccharolyticus JCM 8878T and H. salifodinae JCM 9578T was 46 and 44 %, respectively. The major polar lipids were archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 archaeol, and sulfated diglycosyl archaeol-1. Several unidentified glycolipids were present. Based on the phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halococcus , for which the name Halococcus agarilyticus sp. nov. is proposed. The type strain is 62ET ( = JCM 19592T = KCTC 4143T).

Halocalculus aciditolerans gen. nov., sp. nov., an acid-tolerant haloarchaeon isolated from commercial salt

Three halophilic archaeal strains, MH2-243-1T, MH2-93-1 and MH2-91-1 were isolated from commercial salt samples from Japan, Australia, and Bolivia. Strain MH2-243-1T was able to grow in the presence of 12–30 % (w/v) NaCl (optimum, 18 % NaCl), at pH 4.5–7.0 (optimum, pH 6.0) and at 20–60 °C (optimum, 40 °C). Strains MH2-91-1 and MH2-93-1 grew in slightly different ranges. The orthologous 16S rRNA gene sequences of the three strains were almost identical (99.8–99.9 % similarities), and the closest relative was Salarchaeum japonicum JCM 16327T with 94.2–94.3 % 16S rRNA gene sequence similarities, followed by strains of members of the closely related genera Halobacterium and Halarchaeum . The RNA polymerase subunit B′ gene (rpoB′) sequence also showed the highest similarity (86.6 %) to that of Salarchaeum japonicum JCM 16327T. The DNA G+C contents of strains MH2-243-1T, MH2-93-1 and MH2-91-1 were 68.5, 68.8 and 68.3 mol%, respectively. DNA–DNA relatedness values amongst the three strains were 97–99 %. The polar lipids of the three strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and at least seven unidentified glycolipids. The polar lipid composition differed from those of Salarchaeum japonicum and species of the genera Halobacterium and Halarchaeum . Based on the phenotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of a new genus, for which the name Halocalculus aciditolerans gen. nov., sp. nov. is proposed. The type strain of the type species is MH2-243-1T ( = JCM 19596T = KCTC 4149T) isolated from solar salt produced in Japan. MH2-93-1 ( = JCM 19595) and MH2-91-1 ( = JCM 19594) are additional strains of the type species.

Characterization of Cold- and High-Pressure-Active Polygalacturonases from a Deep-Sea Yeast,Cryptococcus liquefaciensStrain N6

A deep-sea yeast, Cryptococcus liquefaciens strain N6, produces two polygalacturonases, p36 and p40 (N6-PGases). These N6-PGases were highly active at 0-10 degrees C in comparison to a PGase from Aspergillus japonicus. The hydrolytic activity of these N6-PGases remained almost unchanged up to a hydrostatic pressure of 100 MPa at 24 degrees C with a very small activation volume of -1.1 ml/mol. At 10 degrees C, however, the activation volume increased to 3.3 or 5.4 ml/mol (p36 and p40, respectively), suggesting that the enzyme-substrate complexes can expand at their transition states. We speculate that such a volume expansion upon forming the enzyme-substrate complexes contributes to decreasing the activation energy for hydrolysis. This can account for the high activity of N6-PGases at low-temperature.

Alicyclobacillus cellulosilyticus sp. nov., a thermophilic, cellulolytic bacterium isolated from steamed Japanese cedar chips from a lumbermill

A thermophilic bacterium, strain Sueoka(T), was isolated from steamed Japanese cedar chips from a lumber mill in Gobo, Japan. The strain was able to grow on carboxymethyl cellulose at 60 °C, was Gram-stain-negative, and grew between 40.0 and 67.5 °C (optimum at 55 °C) and between pH 3.5 and 6.5 (optimum at pH 4.8). Comparative analysis of 16S rRNA gene sequences revealed 91.9 , 90.9 , and 90.8% similarity to Alicyclobacillus macrosporangiidus(T), Alicyclobacillus pomorum(T), and Alicyclobacillus acidocaldarius(T), respectively. The major quinone was MK-7 and the predominant cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 60.8 mol%. Based on the results of this study, strain Sueoka(T) is a novel species of the genus Alicyclobacillus, and the namehttp://dx.doi.org/10.1601/nm.5071Alicyclobacillus cellulosilyticus sp. nov. (type strain Sueoka(T)  = JCM 18487(T)  = KCTC 33007(T)) is proposed.

Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples

Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative. Two strains were pink–red pigmented, while four other strains were orange–pink pigmented. Strain MH1-16-3T was able to grow at 9–30 % (w/v) NaCl [with optimum at 18 % (w/v) NaCl], at pH 4.5–6.8 (optimum, pH 5.5) and at 20–50 °C (optimum, 42 °C). The five other strains grew at slightly different ranges. The six strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of the six strains were almost identical, sharing 99.9 (1–2 nt differences) to 100 % similarity. The closest relatives were Halarchaeum acidiphilum MH1-52-1T and Halarchaeum salinum MH1-34-1T with 97.7 % similarity. The DNA G+C contents of the six strains were 63.2–63.7 mol%. Levels of DNA–DNA relatedness amongst the six strains were 79–86 %, while those between MH1-16-3T and H. acidiphilum MH1-52-1T and H. salinum MH1-34-1T were both 43 and 45 % (reciprocally), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the six isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum rubridurum sp. nov. is proposed. The type strain is MH1-16-3T ( = JCM 16108T = CECT 7535T).

Thermophilic and halophilic β-agarase from a halophilic archaeon Halococcus sp. 197A

An agar-degrading archaeon Halococcus sp. 197A was isolated from a solar salt sample. The agarase was purified by hydrophobic column chromatography using a column of TOYOPEARL Phenyl-650 M. The molecular mass of the purified enzyme, designated as Aga-HC, was ~55 kDa on both SDS-PAGE and gel-filtration chromatography. Aga-HC released degradation products in the order of neoagarohexose, neoagarotetraose and small quantity of neoagarobiose, indicating that Aga-HC was a β-type agarase. Aga-HC showed a salt requirement for both stability and activity, being active from 0.3 M NaCl, with maximal activity at 3.5 M NaCl. KCl supported similar activities as NaCl up to 3.5 M, and LiCl up to 2.5 M. These monovalent salts could not be substituted by 3.5 M divalent cations, CaCl2 or MgCl2. The optimal pH was 6.0. Aga-HC was thermophilic, with optimum temperature of 70 °C. Aga-HC retained approximately 90 % of the initial activity after incubation for 1 hour at 65-80 °C, and retained 50 % activity after 1 hour at 95 °C. In the presence of additional 10 mM CaCl2, approximately 17 % remaining activity was detected after 30 min at 100 °C. This is the first report on agarase purified from Archaea.

Halarchaeum nitratireducens sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt

Two halophilic moderately acidophilic archaeal strains, MH1-136-2(T) and MH1-370-1 were isolated from commercial salt samples made from seawater in Japan and Indonesia, respectively. Cells of the two strains were pleomorphic and Gram-stain-negative. Strain MH1-136-2(T) was pink pigmented, while MH1-370-1 was orange-red pigmented. Strain MH1-136-2(T) was able to grow at 9-30 % (w/v) NaCl (with optimum, 21 % NaCl, w/v) at pH 4.5-6.2 (optimum, pH 5.2-5.5) and at 18-55 °C (optimum, 45 °C). Strain MH1-370-1 was able to grow at 12-30 % (w/v) NaCl (optimum, 18 %, w/v) at pH 4.2-6.0 (optimum, pH 5.2-5.5) and 20-50 °C (optimum, 45 °C). Strain MH1-136-2(T) required at least 1 mM Mg(2+), while MH1-370-1 required at least 10 mM for growth. Both strains reduced nitrate and nitrite under aerobic conditions. The 16S rRNA gene sequences of strains MH1-136-2(T) and MH1-370-1 were identical, and the closest relative was Halarchaeum rubridurum MH1-16-3(T) with 98.3 % similarity. The level of DNA-DNA relatedness between these strains was 90.9 % and 92.4 % (reciprocally), while that between MH1-136-2(T) and Halarchaeum acidiphilum MH1-52-1(T), Halarchaeum salinum MH1-34-1(T) and Halarchaeum rubridurum MH1-16-3(T) was 37.7 %, 44.3 % and 41.1 % (each an average), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates represent a novel species of the genus Halarchaeum, for which the name Halarchaeum nitratireducens sp. nov. is proposed. The type strain is MH1-136-2(T) ( = JCM 16331(T) = CECT 7573(T)) isolated from solar salt produced in Japan.

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

A novel halophilic strain, BNERC31(T), was isolated from solar salt, 'Sel marin de Guérande', imported from France. Colonies on agar medium containing soluble starch, sodium citrate, sodium glutamate and inorganic salts were non-pigmented and transparent, while cells obtained by centrifuging liquid cultures were red-pigmented. Cells of strain BNERC31(T) were non-motile, pleomorphic, stained Gram-negative and lysed in distilled water. Growth occurred with 20-30 % (w/v) NaCl (optimum, 25 %, w/v), with 0-500 mM MgCl2 (optimum, 10 mM), at pH 6.0-8.5 (optimum, pH 7.0) and at 25-55 °C (optimum, 40 °C). Growth was dependent on soluble starch, and inhibited completely by 0.5 % organic nutrients, such as Casamino acids or yeast extract. The DNA G+C content was 64.1 mol%. Strain BNERC31(T) possessed at least two heterogeneous 16S rRNA genes, and the sequence of the orthologous gene (preceded by the dihydroorotate oxidase gene, pyrD) showed the highest similarity (96.5 %) to that of Haloarcula marismortui JCM 8966(T). The RNA polymerase subunit B' gene sequence showed the highest similarity (91.7 %) to that of Haloarcula amylolytica JCM 13557(T). The polar lipids of strain BNERC31(T) were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, diglycosyl diether and sulfated diglycosyl diether, similar to those of species of the genus Halomicrobium. The phenotypic and phylogenetic characteristics showed that strain BNERC31(T) differed from species of the genera Haloarcula and Halomicrobium and indicated that it represents a novel species in a new genus, for which the name Halomicroarcula pellucida gen. nov., sp. nov. is proposed. The type strain of the type species is BNERC31(T) ( = JCM 17820(T) = CECT 7537(T)).

Marinococcus tarijensis sp. nov., a moderately halophilic bacterium isolated from a salt mine

A Gram-stain-positive, coccoid-shaped, halophilic bacterium, strain SR-1(T), was isolated from a salt crystal obtained from a mine located in Tarija, Bolivia. The strain was investigated using a polyphasic approach. The optimum conditions for growth of strain SR-1(T) were reached at 5% (w/v) NaCl, pH 7.6 and 37-40 °C. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone was MK-7. The major cellular fatty acids of strain SR-1(T) were anteiso-C(15:0), anteiso-C(17:0) and iso-C(16:0). The DNA G+C content of strain SR-1(T) was 48.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed a close relationship between strain SR-1(T) and Marinococcus halophilus JCM 2479(T) (99.7% 16S rRNA gene sequence similarity), Marinococcus halotolerans KCTC 19045(T) (99.4%) and Marinococcus luteus KCTC 13214(T) (99.8%). However, strain SR-1(T) also showed low levels of DNA-DNA relatedness with these reference strains (47, 61 and 58%, respectively). On the basis of phenotypic differences and DNA-DNA hybridization results, strain SR-1(T) is considered to represent a novel species of the genus Marinococcus, for which the name Marinococcus tarijensis sp. nov. is proposed. The type strain is SR-1(T) ( =LMG 26930(T) =CECT 8130(T)).

Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt

Two extremely halophilic archaea, strains MGY-184T and MGY-205, were isolated from sea salt produced in Japan and rock salt imported from Bolivia, respectively. Both strains were pleomorphic, non-motile, Gram-negative and required more than 5 % (w/v) NaCl for growth, with optimum at 9–12 %, in the presence of 2 % (w/v) MgCl2 . 6H2O. In the presence of 18 % (w/v) MgCl2 . 6H2O, however, both strains showed growth even at 1.0 % (w/v) NaCl. Both strains possessed two 16S rRNA genes (rrnA and rrnB), and they revealed closest similarity to Halobaculum gomorrense JCM 9908T, the single species with a validly published name of the genus Halobaculum , with similarity of 97.8 %. The rrnA and rrnB genes of both strains were 100 % similar. The rrnA genes were 97.6 % similar to the rrnB genes in both strains. DNA G+C contents of strains MGY-184T and MGY-205 were 67.0 and 67.4 mol%, respectively. Polar lipid analysis revealed that the two strains contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester derived from C20C20 archaeol. The DNA–DNA hybridization value between the two strains was 70 % and both strains showed low levels of DNA–DNA relatedness (48–50 %) with Halobaculum gomorrense JCM 9908T. Physiological and biochemical characteristics allowed differentiation of strains MGY-184T and MGY-205 from Halobaculum gomorrense JCM 9908T. Therefore, strains MGY-184T and MGY-205 represent a novel species of the genus Halobaculum , for which the name Halobaculum magnesiiphilum sp. nov. is proposed; the type strain is MGY-184T ( = JCM 17821T = KCTC 4100T).

Halarchaeum salinum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt

Three halophilic archaeal strains, MH1-34-1T, MH1-16-1 and MH1-224-5 were isolated from commercial salt samples produced from seawater in Indonesia, the Philippines and Japan, respectively. Cells of the three strains were pleomorphic and stained Gram-negative. Strain MH1-34-1T was orange–red pigmented, while MH1-16-1 and MH1-224-5 were pink-pigmented. Strain MH1-34-1T was able to grow at 12–30 % (w/v) NaCl (with optimum at 18 % NaCl, w/v) at pH 4.5–7.2 (optimum, pH 5.2–5.5) and at 15–45 °C (optimum, 42 °C). Strains MH1-16-1 and MH1-224-5 grew in slightly different ranges. These strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of strains MH1-34-1T, MH1-16-1 and MH1-224-5 were almost identical (99.8–99.9 % similarities), and the closest relative was Halarchaeum acidiphilum MH-1-52-1T with 98.4 % similarities. The DNA G+C contents of MH1-34-1T, MH1-16-1 and MH1-224-5 were 59.3, 60.8 and 61.0 mol%, respectively. The level of DNA–DNA relatedness amongst the three strains was 90–91 %, while that between each of the three strains and Halarchaeum acidiphilum MH1-52-1T was 51–55 %. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolates should represent a novel species of the genus Halarchaeum , for which the name Halarchaeum salinum sp. nov. is proposed. The type strain is MH1-34-1T ( = JCM 16330T = CECT 7574T).

Salinisphaera japonica sp. nov., a moderately halophilic bacterium isolated from the surface of a deep-sea fish, Malacocottus gibber, and emended description of the genus Salinisphaera

A moderately halophilic, slightly acidophilic, aerobic bacterium, designated strain YTM-1(T), was isolated from the body surface of Malacocottus gibber. Cells were Gram-stain-negative, short rods or cocci, approximately 0.9-1.1 µm long and 1.0-1.8 µm wide. Strain YTM-1(T) was able to grow with 1-30% NaCl (optimum, 7.5-10%, w/v), at 4-30 °C (optimum, 20-25 °C) and at pH 3.8-9.5 (optimum, pH 5.0-5.5). Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain YTM-1(T) belonged to the genus Salinisphaera with low similarity values to the type strains of recognized species of this genus (<94.8-94.4%). The polar lipids of strain YTM-1(T) consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unknown phospholipids and one unknown lipid. The predominant isoprenoid quinone was Q-8. The major fatty acids were C19:0ω8c cyclo, C18:1ω7c, C16:1ω5c and C16:0. The DNA G+C content of strain YTM-1(T) was 67.3 mol%. These phylogenetic, physiological and chemotaxonomic data indicated that strain YTM-1(T) represents a novel species of the genus Salinisphaera, for which the name Salinisphaera japonica sp. nov. is proposed. The type strain is YTM-1(T) (=JCM 18087(T)=CECT 8012(T)). An emended description of the genus Salinisphaera is also proposed.

Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957

Halobacterium piscisalsi was proposed by Yachai et al. (2008), with a single strain, HPC1-2T ( = BCC 24372T  = JCM 14661T  = PCU 302T), which was isolated from fermented fish (pla-ra) in Thailand. According to Yachai et al. (2008), the strain was closely related to Halobacterium salinarum based on 16S rRNA gene sequence comparisons and could be differentiated by low DNA–DNA relatedness values and different biochemical profiles compared with other species of the genus. The reanalysis of the 16S rRNA gene sequences and the DNA–DNA relatedness among H. piscisalsi JCM 14661T and H. salinarum strains JCM 8978T, R1 and NRC-1 revealed that they all had exactly the same 16S rRNA gene sequence and shared more than 70 % DNA–DNA relatedness. In addition, the full-length DNA-dependent RNA polymerase subunit B (RpoB) protein sequence of H. piscisalsi JCM 14661T (607 amino acids) was the same as that of H. salinarum JCM 8978T and showed 94.7 and 96.7 % similarities with those of Halobacterium noricense JCM 15102T and Halobacterium jilantaiense JCM 13558T, respectively. Despite the different biochemical properties described by Yachai et al. (2008), the characteristic phenotypic properties of H. piscisalsi agreed with those in the description of H. salinarum emended by Gruber et al. (2004). Therefore, H. piscisalsi Yachai et al. (2008) should be regarded as a later heterotypic synonym of H. salinarum Elazari-Volcani 1957.

Natronoarchaeum philippinense sp. nov., a haloarchaeon isolated from commercial solar salt

A Gram-staining-negative, pleomorphic, aerobic, halophilic archaeon, designated strain 294-194-5(T), was isolated in Japan from commercial solar salt imported from the Philippines. Colonies of strain 294-194-5(T) were translucent and red. Strain 294-194-5(T) was able to grow at 20-50 °C (optimum, 37-45 °C), with 14-30 % (w/v) NaCl (optimum, 18 %), and at pH 6.5-8.5 (optimum, pH 8.0). MgCl2 was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain 294-194-5(T) was most closely related to Natronoarchaeum mannanilyticum YSM-123(T) (96.8-97.1 % sequence similarities). The major polar lipids of the novel strain were the C20C20 and C20C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester and the same glycolipids (disulfated diglycosyl diether and one unidentified glycolipid) as detected in N. mannanilyticum YSM-123(T). The DNA G+C content of strain 294-194-5(T) was 63.0 mol%. The DNA-DNA relatedness values between the novel strain and N. mannanilyticum YSM-123(T)were 46.5 % and 48.5 % (reciprocal). Based on these data, strain 294-194-5(T) represents a novel species of the genus Natronoarchaeum, for which the name Natronoarchaeum philippinense sp. nov. is proposed. The type strain is 294-194-5(T) ( = JCM 16593(T) = CECT 7630(T)).

Natribacillus halophilus gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium isolated from soil

A moderately halophilic and alkalitolerant bacterium, designated strain HN30T, was isolated from garden soil in Japan. Cells of strain HN30T were motile, endospore-forming, aerobic, rod-shaped and Gram-positive, and contained A1γ meso-diaminopimelic acid-type murein. Growth occurred in 7–23 % (w/v) NaCl (optimum, 10–15 %, w/v), at pH 6.5–10.0 (optimum, pH 8.0–8.5) and at 20–40 °C (optimum, 30 °C). The isoprenoid quinone was menaquinone-7. The polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of strain HN30T was 47 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HN30T was most closely related to Geomicrobium halophilum BH1T (93 % sequence similarity). 16S rRNA gene sequence similarities with other recognized species were less than 89 %. Phylogenetic and phenotypic characteristics indicated that strain HN30T represents a novel species in a new genus, for which the name Natribacillus halophilus gen. nov., sp. nov. is proposed; the type strain is HN30T ( = JCM 15649T = DSM 21771T).

Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups

In many prokaryotic species, 16S rRNA genes are present in multiple copies, and their sequences in general do not differ significantly owing to concerted evolution. At the time of writing, the genus Haloarcula of the family Halobacteriaceae comprises nine species with validly published names, all of which possess two to four highly heterogeneous 16S rRNA genes. Existence of multiple heterogeneous 16S rRNA genes makes it difficult to reconstruct a biological phylogenetic tree using their sequence data. If the orthologous gene is able to be discriminated from paralogous genes, a tree reconstructed from orthologous genes will reflect a simple biological phylogenetic relationship. At present, however, we have no means to distinguish the orthologous rRNA operon from paralogous ones in the members of the family Halobacteriaceae. In this study, we found that the dihydroorotate oxidase gene, pyrD, was present in the immediate upstream of one 16S rRNA gene in each of ten strains of the family Halobacteriaceae whose genome sequences have been determined, and the direction of the pyrD gene was opposite to that of the 16S rRNA genes. In two other strains whose genome sequences have been determined, the pyrD gene was present in far separated positions. We designed PCR primer sets to amplify DNA fragments encompassing a region from the conserved region of the pyrD gene to a conserved region of the tRNA-Ala gene or the 23S rRNA gene to determine the 16S rRNA gene sequences preceded by the pyrD gene, and to see if the pyrD gene is conserved in the immediate upstream of rRNA operon(s) in the type strains of the type species of 28 genera of the family Halobacteriaceae. Seventeen type strains, including the ten strains mentioned above, gave amplified DNA fragments of approximately 4000 bp, while eleven type strains, including the two strains mentioned above, did not give any PCR products. These eleven strains are members of the Clade I haloarchaea, originally defined by Walsh et al. (2004) and expanded by Minegishi et al. (2010). Analysis of contig sequences of three strains belonging to the Clade I haloarchaea also revealed the absence of the pyrD gene in the immediate upstream of any 16S rRNA genes. It may be scientifically sound to hypothesize that during the evolution of members of the family Halobacteriaceae, a pyrD gene transposition event happened in one group and this was followed by subsequent speciation processes in each group, yielding species/genera of the Clade I group and ‘the rest’ of the present family Halobacteriaceae.

A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales

Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, the Halobacteriales is a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of the Halobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genus Haloarcula was analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic level within the Halobacteriales.

Halostagnicola alkaliphila sp. nov., an alkaliphilic haloarchaeon from commercial rock salt

A Gram-negative, pleomorphic, aerobic, haloalkaliphilic archaeon, strain 167-74T, was isolated from commercial rock salt imported into Japan from China. Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain 167-74T is closely related to Halostagnicola larsenii XH-48T (98.3 %) and Halostagnicola kamekurae 194-10T (97.2 %). The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. A glycolipid was not detected, in contrast to the two existing, neutrophilic species of the genus Halostagnicola. The DNA G+C content of strain 167-74T was 60.7 mol%. and it gave DNA–DNA reassociation values of 19.5 and 18.8 %, respectively, with Hst. larsenii JCM 13463T and Hst. kamekurae 194-10T. Therefore, strain 167-74T represents a novel species, for which the name Halostagnicola alkaliphila sp. nov. is proposed, with the type strain 167-74T ( = JCM 16592T  = CECT 7631T).

Natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt

Strain YSM-123T was isolated from commercial salt made from Japanese seawater in Niigata prefecture. Optimal NaCl and Mg2+ concentrations for growth were 4.0–4.5 M and 5 mM, respectively. The isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and pH were 37 °C and pH 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence analysis suggested that strain YSM-123T is a member of the phylogenetic group defined by the family Halobacteriaceae, but there were low similarities to type strains of other genera of this family (≤90 %); for example, Halococcus (similarity <89 %), Halostagnicola (<89 %), Natronolimnobius (<89 %), Halobiforma (<90 %), Haloterrigena (<90 %), Halovivax (<90 %), Natrialba (<90 %), Natronobacterium (<90 %) and Natronococcus (<90 %). The G+C content of the DNA was 63 mol%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, disulfated diglycosyl diether and an unknown glycolipid. On the basis of the data presented, we propose that strain YSM-123T should be placed in a new genus and species, Natronoarchaeum mannanilyticum gen. nov., sp. nov. The type strain of Natronoarchaeum mannanilyticum is strain YSM-123T (=JCM 16328T =CECT 7565T).

Salarchaeum japonicum gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea isolated from commercial salt

Strain YSM-79(T) was isolated from commercial salt made from seawater in Yonaguni island, Okinawa, Japan. The strain is an aerobic, Gram-negative, chemo-organotrophic and extremely halophilic archaeon. Cells are short rods that lyse in distilled water. Growth occurs at 1.5-5.3 M NaCl (optimum 2.5-3.0 M), pH 5.0-8.8 (optimum pH 5.2-6.3) and 20-55 °C (optimum 40 °C). Mg²⁺ is required for growth, with maximum growth at 200-300 mM Mg²⁺. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, sulfated diglycosyl diether-1 and five unidentified glycolipids. The G+C content of the DNA was 64 mol%. On the basis of 16S rRNA gene sequence analysis, strain YSM-79(T) was determined to be a member of the family Halobacteriaceae, with the closest related genus being Halobacterium (94 % sequence identity). In addition, the rpoB' gene sequence of strain YSM-79(T) had <88 % sequence similarity to those of other members of the family Halobacteriaceae. The results of phenotypic, chemotaxonomic and phylogenetic analysis suggested that strain YSM-79(T) should be placed in a new genus, Salarchaeum gen. nov., as a representative of Salarchaeum japonicum sp. nov. The type strain is YSM-79(T) ( = JCM 16327(T)  = CECT 7563(T)).

Halostagnicola kamekurae sp. nov., an extremely halophilic archaeon from solar salt

A novel extremely halophilic archaeon, strain 194-10(T), was isolated from a solar salt sample imported into Japan from the Philippines. Strain 194-10(T) was pleomorphic, neutrophilic and mesophilic and required at least 10 % (w/v) NaCl but no MgSO(4) . 7H(2)O for growth; it exhibited optimal growth at 15 % (w/v) NaCl and 60 mM MgSO(4) . 7H(2)O. Strain 194-10(T) grew at 20-45°C (optimum, 30°C) and pH 6.0-9.0 (optimum, pH 6.5-7.0). The G+C content of its DNA was 59.8 mol%. 16S rRNA gene sequence analysis revealed closest proximity to Halostagnicola larsenii XH-48(T) (98.5 % similarity), the sole representative of the genus Halostagnicola. Polar lipid analysis revealed that strain 194-10(T) contained phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester (the latter derived from both C(20)C(20) and C(20)C(25) archaeol) and several unidentified glycolipids. The results of DNA-DNA hybridization (20.7 % relatedness between Hst. larsenii JCM 13463(T) and strain 194-10(T)) and physiological and biochemical characteristics allowed differentiation of strain 194-10(T) from Hst. larsenii XH-48(T). Therefore, strain 194-10(T) represents a novel species of the genus Halostagnicola, for which the name Halostagnicola kamekurae sp. nov. is proposed, with the type strain 194-10(T) (=DSM 22427(T) =JCM 16110(T) =CECT 7536(T)).

Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt

A novel halophilic archaeon, strain MH1-52-1(T), was isolated from solar salt imported from Australia. Cells were pleomorphic, non-motile and Gram-negative. Strain MH1-52-1(T) required at least 3.0 M NaCl and 1 mM Mg(2+) for growth. Strain MH1-52-1(T) was able to grow at pH 4.0-6.0 (optimum, pH 4.4-4.5) and 15-45 °C (optimum, 37 °C). The diether phospholipids phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C(20)C(20) and C(20)C(25) archaeol, were present. Four unidentified glycolipids were also detected. The 16S rRNA gene sequence showed the highest similarity to that of Halobacterium noricense A1(T) (91.7%); there were lower levels of similarity to other members of the family Halobacteriaceae. The G+C content of its DNA was 61.4 mol%. Based on our phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate should be classified as a representative of a new genus and species, for which the name Halarchaeum acidiphilum gen. nov., sp. nov. is proposed. The type strain of Halarchaeum acidiphilum is MH1-52-1(T) (=JCM 16109(T) =DSM 22442(T) =CECT 7534(T)).

Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene

A considerable number of species of the Halobacteriaceae possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera Haloterrigena and Natrinema show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus Natrialba form definitely separate clusters in neighbour-joining trees, suggesting that these two clusters could be separated into two genera. In an attempt to solve these problems, the RNA polymerase B' subunit has been used as an additional target molecule for phylogenetic analysis, using partial sequences of 1305 bp. In this work, a primer set was designed that consistently amplified the full-length RNA polymerase B' subunit gene (rpoB') (1827-1842 bp) from 85 strains in 27 genera of the Halobacteriaceae. Differences in sequence length were found within the first 15 to 31 nt, and their downstream sequences (1812 bp) were aligned unambiguously without any gaps or deletions. Phylogenetic trees reconstructed from nucleotide sequences and deduced amino acid sequences by the maximum-likelihood method demonstrated that multiple species/strains in most genera individually formed cohesive clusters. Two discrepancies were observed: (i) the two species of Natronolimnobius were placed in definitely different positions, in that Natronolimnobius innermongolicus was placed in the Haloterrigena/Natrinema cluster, while Natronolimnobius baerhuensis was closely related to Halostagnicola larsenii, and (ii) Natronorubrum tibetense was segregated from the three other Natronorubrum species in the protein tree, while all four species formed a cluster in the gene tree, although supported by a bootstrap value of less than 50 %. The six Haloterrigena species/strains and the five species of Natrinema formed a large cluster in both trees, with Halopiger xanaduensis and Nln. innermongolicus located in the cluster in the protein tree and Nln. innermongolicus in the gene tree. Hpg. xanaduensis broke into the cluster of the genus Halobiforma, instead of the Haloterrigena/Natrinema cluster, in the gene tree. The six Natrialba species formed a tight cluster with two subclusters, of neutrophilic species and alkaliphilic species, in both trees. Overall, our data strongly suggest that (i) Nln. innermongolicus is a member of Haloterrigena/Natrinema, (ii) Nrr. tibetense might represent a new genus and (iii) the two genera Haloterrigena and Natrinema might constitute a single genus. As more and more novel species and genera are proposed in the family Halobacteriaceae, the full sequence of the rpoB' gene may provide a supplementary tool for determining the phylogenetic position of new isolates.

Natronorubrum sediminis sp. nov., an archaeon isolated from a saline lake

Two novel haloalkaliphilic archaea, strains CG-6T and CG-4, were isolated from sediment of the hypersaline Lake Chagannor in Inner Mongolia, China. Cells of the two strains were pleomorphic, non-motile and strictly aerobic. They required at least 2.5 M NaCl for growth, with optimum growth at 3.4 M NaCl. They grew at pH 8.0-11.0, with optimum growth at pH 9.0. Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. The two strains had similar polar lipid compositions, possessing C20C20 and C20C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. No glycolipids were detected. Comparison of 16S rRNA gene sequences and morphological features placed them in the genus Natronorubrum. 16S rRNA gene sequence similarities to strains of recognized species of the genus Natronorubrum were 96.2-93.8%. Detailed phenotypic characterization and DNA-DNA hybridization studies revealed that the two strains belong to a novel species in the genus Natronorubrum, for which the name Natronorubrum sediminis sp. nov. is proposed; the type strain is CG-6T (=CECT 7487T =CGMCC 1.8981T =JCM 15982T).

Natronomonas moolapensis sp. nov., non-alkaliphilic isolates recovered from a solar saltern crystallizer pond, and emended description of the genus Natronomonas

Two isolates of non-alkaliphilic, extremely halophilic archaea, with very similar characteristics, were recovered from a marine solar saltern crystallizer. Cells were pleomorphic, motile and Gram-stain-negative and grew on a limited range of carbon sources, with pyruvate being the best substrate. Optimum growth occurred at 18-20 % (w/v) NaCl, pH 6.0-8.5 and 37-40 degrees C. Both isolates possessed typical archaeal lipids, and their 16S rRNA gene sequences were 99.8 % identical. Phylogenetic tree reconstructions indicated that they were most closely related to the haloalkaliphile Natronomonas pharaonis (97.5 % similarity to the type strain), but the different phenotypic properties and low DNA-DNA hybridization values between Nmn. pharaonis DSM 2160(T) and the two isolates suggested that they represent a novel species within the genus Natronomonas. The name Natronomonas moolapensis sp. nov. is proposed for these isolates, with the type strain being 8.8.11(T) (=JCM 14361(T) =CECT 7526(T) =DSM 18674(T)). An emended description of the genus Natronomonas is also provided.

Geomicrobium halophilum gen. nov., sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from soil

Two moderately halophilic and alkaliphilic bacteria, designated strains BH1(T) and HN5, were isolated from forest soil and garden soil, respectively, in Japan. Cells of strains BH1(T) and HN5 were non-motile, aerobic, bean-shaped, formed irregular clusters with 2-20 cells, Gram-positive and contained A1gamma, meso-diaminopimelic acid-type murein. Spore formation was not detected. Growth occurred in 5-25 % (w/v) NaCl (optimum, 10-15 %, w/v), at pH 6.0-10.0 (optimum, pH 8.5-9.0) and at 20-40 degrees C (optimum, 30 degrees C). The predominant isoprenoid quinones were menaquinone-7 and menaquinone-6. The phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were i-C(15 : 0), i-C(17 : 0) and i-C(18 : 0). The DNA G+C content of strains BH1(T) and HN5 was 45 and 46 mol%, respectively. The 16S rRNA gene sequences of the two strains were 99.9 % similar. DNA-DNA hybridization results indicated high levels of relatedness (88 and 85 % reciprocally). Similarities with recognized species were less than 90.2 %. The phylogenetic and phenotypic characteristics indicated that strains BH1(T) and HN5 represent a novel species in a new genus, for which the name Geomicrobium halophilum gen. nov., sp. nov. is proposed. The type strain is BH1(T) (=JCM 15647(T)=DSM 21769(T)).

Acidophilic haloarchaeal strains are isolated from various solar salts

Haloarchaeal strains require high concentrations of NaCl for their growth, with optimum concentrations of 10–30%. They display a wide variety of morphology and physiology including pH range for growth. Many strains grow at neutral to slightly alkaline pH, and some only at alkaline pH. However, no strain has been reported to grow only in acidic pH conditions within the family Halobacteriaceae.

In this study, we isolated many halophiles capable of growth in a 20% NaCl medium adjusted to pH 4.5 from 28 commercially available salts. They showed growth at pH 4.0 to 6.5, depending slightly on the magnesium content. The most acidophilic strain MH1-52-1 isolated from an imported solar salt (pH of saturated solution was 9.0) was non-pigmented and extremely halophilic. It was only capable of growing at pH 4.2–4.8 with an optimum at pH 4.4 in a medium with 0.1% magnesium chloride, and at pH 4.0–6.0 (optimum at pH 4.0) in a medium with 5.0% magnesium. The 16S rRNA and DNA-dependent RNA polymerase subunit B' gene sequences demonstrated clearly that the strain MH1-52-1 represents a new genus in the family Halobacteriaceae.

Systematic analysis of HSP gene expression and effects on cell growth and survival at high hydrostatic pressure in Saccharomyces cerevisiae

We systematically investigated the role of HSP genes in the growth and survival of Saccharomyces cerevisiae under high hydrostatic pressure together with analysis of pressure-regulated gene expression. Cells of strain BY4742 were capable of growth at moderate pressure of 25 MPa. When pressure of 25 MPa was applied to the cells, the expression of HSP78, HSP104, and HSP10 was upregulated by about 3- to 4-fold, and that of HSP32, HSP42, and HSP82 was upregulated by about 2- to 2.6-fold. However, the loss of one of the six genes did not markedly affect growth at 25 MPa, while the loss of HSP31 impaired high-pressure growth. These results suggest that Hsp31 plays a role in high-pressure growth but that the six upregulated genes do not. Extremely high pressure of 125 MPa decreased the viability of the wild-type cells to 1% of the control level. Notably, the loss of HSP genes other than HSP31 enhanced the survival rate by about fivefold at 125 MPa, suggesting that the cellular defensive system against high pressure could be strengthened upon the loss of the HSP genes. In this paper, we describe the requirement for and significance of a subset of HSP genes in yeast cell growth at moderate pressure and survival at extremely high pressure.

Pattern recognition as a caring partnership in families with cancer

Pattern recognition as a caring partnership in families with cancer The purpose of this study was to address the process of a caring partnership by elaborating pattern recognition as nursing intervention with families with cancer. It is based on Newman's theory of health as expanding consciousness within the unitary-transformative paradigm and is an extension of a previous study of Japanese women with ovarian cancer. A hermeneutic, dialectic method was used to engage 10 Japanese families in which the wife-mothers were hospitalized because of cancer diagnosis. The family included at least the woman with cancer and her primary caregiver. Each of four nurse-researchers entered into partnership with a different family and conducted three interviews with each family. The participants were asked to describe the meaningful persons and events in their family history. The family's story was transmuted into a diagram of sequential patterns of interactional configurations and shared with the family at the second meeting. Evidence of pattern recognition and insight into the meaning of the family pattern were identified further in the remaining meetings. The data revealed five dimensions of a transformative process. Most families found meaning in their patterns and made a shift from separated individuals within the family to trustful caring relationships. One-third of them went through this process within two interviews. The families showed increasing openness, connectedness and trustfulness in caring relationships. In partnership with the family, each nurse-researcher grasped the pattern of the family as a whole and experienced the meaning of caring. Pattern recognition as nursing intervention was a meaning-making transforming process in the family-nurse partnership.