Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34021 and Halobacterium lacusprofundi to the Genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrum sodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb. nov

Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments

BACKGROUND

Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typical cold regions such as the remote Arctic and Antarctic are rare, and the limited number of high-quality genomes available leaves us with little data on genomic traits that are statistically associated with cold environmental conditions.

RESULTS

In this study, we examined the haloarchaeal genus Halorubrum and defined a new clade that represents six isolates from polar and deep earth environments ('PD group' hereafter). The genomic G + C content and amino acid composition of this group distinguishes it from other Halorubrum and the trends are consistent with the established genomic optimization of psychrophiles. The cold adaptation of the PD group was further supported by observations of increased flexibility of proteins encoded across the genome and the findings of a growth test.

CONCLUSIONS

The PD group Halorubrum exhibited denser genome packing, which confers higher metabolic potential with constant genome size, relative to the reference group, resulting in significant differences in carbon, nitrogen and sulfur metabolic patterns. The most marked feature was the enrichment of genes involved in sulfur cycling, especially the production of sulfite from organic sulfur-containing compounds. Our study provides an updated view of the genomic traits and metabolic potential of Halorubrum and expands the range of sources of cold-adapted haloarchaea.

Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov

Currently, there are four mainstream taxonomic opinions on the classification of the class Halobacteria at the family and order levels. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria (ICSP), List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Centre for Biotechnology Information (NCBI) adopted taxonomies have three to four orders and up to eight families, while the Genome Taxonomy Database (GTDB) taxonomy proposes only one order with nine families. To resolve the taxonomic inconsistency, phylogenomic analyses based on concatenated single-copy orthologous proteins and 122 concatenated conserved single-copy marker proteins were conducted to infer the taxonomic status of the current representatives of the class Halobacteria at the family and order levels. The current 76 genera with validly published names of the class Halobacteria were able to be assigned into eight families in one order. On the basis of these results, it is proposed that the current species with validly published names of the class Halobacteria should be remerged into the order Halobacteriales, then assigned to eight families, Haladaptataceae, Haloarculaceae, Halobacteriaceae, Halococcaceae, Haloferacaceae, Natronoarchaeaceae, Natrialbaceae and Halorubellaceae. Thus, Haladaptataceae fam. nov. is described based on Haladaptatus, Halomicrococcus and Halorussus and Halorubellaceae fam. nov. is proposed incorporating Haloarchaeobius and Halorubellus, respectively.

Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions

Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, Antarctica. Hrr. lacusprofundi is commonly used to study adaptation to cold environments and thereby a potential source for biotechnological products. Additionally, in contrast to other haloarchaeal model organisms, Hrr. lacusprofundi is also susceptible to a range of different viruses and virus-like elements, making it a great model to study virus-host interactions in a cold-adapted organism. A genetic system has previously been reported for Hrr. lacusprofundi; however, it does not allow in-frame deletions and multiple gene knockouts. Here, we report the successful generation of uracil auxotrophic (pyrE2) mutants of two strains of Hrr. lacusprofundi. Subsequently, we attempted to generate knockout mutants using the auxotrophic marker for selection. However, surprisingly, only the combination of the auxotrophic marker and antibiotic selection allowed the timely and clean in-frame deletion of a target gene. Finally, we show that vectors established for the model organism Haloferax volcanii are deployable for genetic manipulation of Hrr. lacusprofundi, allowing the use of the portfolio of genetic tools available for H. volcanii in Hrr. lacusprofundi.

Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern

A novel extremely halophilic archaeon, strain RHB-CT, was isolated from a saturated brine pond of a solar saltern in Bolinao, Pangasinan, Philippines. Colonies were orange-red-pigmented, smooth, convex and round on a solid modified growth medium containing 25 % (w/v) of total salts. Cells of strain RHB-CT on the solid modified growth medium were ovoid-shaped (0.89–2.66 µm long), while the cells in a liquid modified growth medium were rod-shaped (1.53–5.65 µm long and 0.45–1.03 µm wide). The strain was Gram-stain-negative, motile and strictly aerobic. Strain RHB-CT grew with NaCl concentrations ranging from 10 to 30 % (w/v; optimum, 20–25 %), at pH 6.5–8.5 (optimum, pH 7.0–7.5) and at 20–55 °C (optimum, 40–45 °C). Furthermore, the strain grew even in the absence of Mg2+; however, when supplemented with Mg2+, growth was observed optimally at 0.2–0.4 M Mg2+. The 16S rRNA gene phylogeny inferred that the strain is a member of the genus Halorubrum and was related to Halorubrum xinjiangense CGMCC 1.3527T (99.0 %), Halorubrum sodomense DSM 3755T (98.8 %), Halorubrum coriense Ch2T (98.8 %), Halorubrum trapanicum NRC 34021T (98.4 %) and Halorubrum distributum JCM 9100T (98.1 %). The rpoB′ gene sequences also showed that strain RHB-CT is related to Hrr. xinjiangense JCM 12388T (97.1 %), Hrr. distributum JCM 9100T (97.1 %), Hrr. coriense JCM 9275T (96.5 %), Hrr. californiense JCM 14715T (96.5 %), Hrr. trapanicum JCM 10477T (96.3%), Hrr. sodomense JCM 8880T (96.2%) and Hrr. tebenquichense DSM 14210T (95.6 %). The DNA G+C content of strain RHB-CT was 68.7 mol% (genome). Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RHB-CT and the closely related species of Halorubrum were below 40 and 90 %, respectively, which are far below the thresholds to delineate a new species. The polar lipids of strain RHB-CT were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and sulfated mannosyl glycosyl diether. Based on dDDH and ANI values, and the significant morphological and physiological differences from known taxa, it is hereby suggested that strain RHB-CT represents a novel species of the genus Halorubrum , for which the name Halorubrum salinarum sp. nov. is proposed. The type strain is RHB-CT (=KCTC 4274T=CMS 2103T).

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.

Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia

A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as Halorubrum, Haloferax, Haloarcula, and Halogeometricum genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. Nanohaloarchaea were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches.

Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996

A comparative taxonomic study of Halorubrum distributum, Halorubrum terrestre, Halorubrum arcis and Halorubrum litoreum was carried out using different approaches, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), phylogenomic analysis based on the comparison of the core genome, orthologous average nucleotide identity (OrthoANI), Genome-to-Genome Distance Calculator (GGDC), synteny plots and polar lipid profile (PLP). The MLSA study, using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB′, and the phylogenomic analysis based on 1347 core translated gene sequences obtained from their genomes showed that Halorubrum distributum JCM 9100^T, Halorubrum terrestre JCM 10247^T, Halorubrum arcis JCM 13916^T and Halorubrum litoreum JCM 13561^T formed a robust cluster, clearly separated from the rest of species of the genus Halorubrum. The OrthoANI and digital DDH values, calculated by the GGDC, showed percentages among Hrr. distributum JCM 9100^T, Hrr. terrestre JCM 10247^T, Hrr. arcis JCM 13916^T and Hrr. litoreum JCM 13561^T that ranged from 98.1 to 97.5 %, and 84.0 to 78.0 %, respectively, while these values among those strains and the type strains of their most related species of Halorubrum were equal or lower than 90.8 and 41.2 %, respectively. Moreover, degree of synteny across the four genomes was very high, especially between the genomes of Halorubrum litoreum JCM 13561^T and Halorubrum arcis JCM 13916^T. In addition, the PLP is quite similar among the four strains studied, showing a common pattern typical of the neutrophilic species of the genus Halorubrum. Overall, these data show that Hrr. distributum, Hrr. terrestre, Hrr. arcis and Hrr. litoreum constitute a single species. Thus, the latter three should be considered as later, heterotypic synonyms of Hrr. distributum based on the rules for priority of names. We propose an emended description of Hrr. distributum, including the features of Hrr. terrestre, Hrr. arcis and Hrr. litoreum.

Halorubrum amylolyticum sp. nov., a novel halophilic archaeon isolated from a salt mine

A pleomorphic and non-motile halophilic archaeon forming light-red pigmented colonies, strain ZC67^T, was isolated from the Yuanyongjing Salt Mine, Yunnan, China. Based on similarity search and phylogenetic analysis of the 16S rRNA gene sequence, strain ZC67^T belongs to the genus Halorubrum and is closely related to the species of Halorubrum (Hrr.) saccharovorum JCM 8865^T, Hrr. persicum C49^T, Hrr. halophilum B8^T, Hrr. lipolyticum 9-3^T, Hrr. salsamenti Y69^T and Hrr. depositum Y78^T with 16S rRNA gene sequence similarities of 99.0%, 98.7%, 98.5%, 98.4%, 98.1% and 97.7%, respectively. The values of average nucleotide identity (ANI) and average amino-acid identity (AAI) between strain ZC67^T and its close relatives were less than 90.5% and 89.3%, respectively. In silico DNA-DNA hybridization (DDH) analysis showed that DNA-DNA relatedness between strain ZC67^T and its relatives is less than 45%. Values of ANI, AAI and in silico DDH were clearly below the thresholds used for the delineation of a new species. The major polar lipids of strain ZC67^T were similar to other neutrophilic members in the genus Halorubrum containing phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl-glucosyl-glycerol diether-1. The DNA G+C content was determined to be 66.3 mol% (based on the draft genome). Combined with other diagnostic characteristics, e.g. phenotypic and chemotaxonomic differences, strain ZC67^T is concluded to represent a novel species in the genus Halorubrum, for which the name Halorubrum amylolyticum sp. nov. is proposed. The type strain is ZC67^T (=CGMCC 1.15718^T = JCM 31850^T).

Draft Genome Sequence of Halorubrum sp. Strain 48-1-W from a Saline Lake in the Novosibirsk Region, Russia

Halorubrum sp. strain 48-1-W was isolated from a water sample from a saline lake (Novosibirsk Region, Russia, 54°14′N 78°13′E).

Halorubrum sp. strain 48-1-W was isolated from a water sample from a saline lake (Novosibirsk Region, Russia, 54°14′N 78°13′E). The sequenced and annotated genome is 3,584,929 bp and contains 3,506 genes.

The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers

Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis.

Halorubrum glutamatedens sp. nov., a Halophilic Archaeon Isolated from a Rock Salt

An extremely halophilic archaeon, strain ZY8^T, was isolated from a rock salt of Yunnan salt mine. It was able to grow at 12-30% (w/v) NaCl (optimum, 15-20%), pH 7.0-9.0 (optimum, pH 8.5), and 20-45 °C (optimum, 42 °C). Sequence similarity search of its 16S rRNA gene showed that strain ZY8^T belonged to the genus Halorubrum, and it is closely related to species of H. aethiopicum SAH-A6^T (98.6%), H. aquaticum EN-2^T (98.6%), and H. halodurans Cb34^T (98.5%), respectively. Strain ZY8^T contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate as its major phospholipids, and a sulfated diglycosyl diether as its major glycolipid. The DNA G+C content was 66.7 mol%. DNA-DNA relatedness between strains ZY8^T and closely related species were far below 70%. Based on the phenotypic and phylogenetic analyses, it is proposed that strain ZY8^T represents a novel species of the genus Halorubrum, for which the name Halorubrum glutamatedens sp. nov. is proposed. The type strain is ZY8^T (=CGMCC 1.16026^T=NBRC 112866^T).

Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006

A polyphasic comparative taxonomic study of Halorubrum ezzemoulense Kharroub et al. 2006, Halorubrum chaoviator Mancinelli et al. 2009 and eight new Halorubrum strains related to these haloarchaeal species was carried out. Multilocus sequence analysis using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB', and phylogenetic analysis based on the 757 core protein sequences obtained from their genomes showed that Hrr. ezzemoulense DSM 17463^T, Hrr. chaoviator Halo-G*^T (=DSM 19316^T) and the eight Halorubrum strains formed a robust cluster, clearly separated from the remaining species of the genus Halorubrum. The orthoANI value and digital DNA-DNA hybridization value, calculated by the Genome-to-Genome Distance Calculator (GGDC), showed percentages among Hrr. ezzemoulense DSM 17463^T, Hrr. chaoviator DSM 19316^T and the eight Halorubrum strains ranging from 99.4 to 97.9 %, and from 95.0 to 74.2 %, respectively, while these values for those strains and the type strains of the most closely related species of Halorubrum were 88.7-77.4 % and 36.1-22.3 %, respectively. Although some differences were observed, the phenotypic and polar lipid profiles were quite similar for all the strains studied. Overall, these data show that Hrr. ezzemoulense, Hrr. chaoviator and the eight new Halorubrum isolates constitute a single species. Thus, Hrr. chaoviator should be considered as a later, heterotypic synonym of Hrr. ezzemoulense. We propose an emended description of Hrr. ezzemoulense, including the features of Hrr. chaoviator and those of the eight new isolates.

Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure

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.

Halorubrum depositum sp. nov., a Novel Halophilic Archaeon Isolated from a Salt Deposit

A non-motile, pleomorphic rod-shaped or oval, red-pigmented (nearly scarlet), extremely halophilic archaeon, strain Y78^T, was isolated from a salt deposit of Yunnan salt mine, China. Analysis of the 16S rRNA gene sequence showed that it was phylogenetically related to species of the genus Halorubrum, with a close relationship to Halorubrum rutilum YJ-18-S1^T (98.6%), Halorubrum yunnanense Q85^T (98.3%), and Halorubrum lipolyticum 9-3^T (98.1%). The temperature, NaCl, and pH ranges for growth were 25-50 °C, 12-30% (w/v), and 6.5-9.0, respectively. Mg²⁺ was required for growth. The polar lipids of strain Y78^T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, and a sulfated diglycosyl diether. The DNA G+C content was 66.6 mol%. DNA-DNA hybridization values between strain Y78^T and two closely related species of the genus Halorubrum were far below 70%. Based on the data presented in this study, strain Y78^T represents a novel species for which the name Halorubrum depositum sp. nov. is proposed; the type strain is Y78^T (= CGMCC 1.15456^T = JCM 31272^T).

Halorubrum salsamenti sp. nov., a Novel Halophilic Archaeon Isolated from a Brine of Salt Mine

A non-motile, spherical or oval extremely halophilic archaeon, strain Y69^T, was isolated from a brine of the Yunnan salt mine, China. Colonies on JCM 168 agar plate were round (1-2 mm in diameter), moist, and orange-pigmented. Phylogenetic analysis of the almost-complete 16S rRNA gene sequence showed that the isolate belonged to the species of the genus Halorubrum, with a close relationship to Halorubrum aidingense 31-hong^T (98.5%), Halorubrum lacusprofundi ATCC 49239^T (98.2%), and Halorubrum kocurii BG-1^T (98.0%). The major polar lipids of strain Y69^T were phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl diether. Strain Y69^T grew in 15-30% (w/v) NaCl. The temperature and pH ranges for growth were 25-50 °C and 6.5-9.0, respectively. Optimal growth occurred at 20% (w/v) NaCl, 42 °C, and pH 8.0. Mg²⁺ was required for growth. The DNA G+C content was determined to be 65.1 mol% by the thermal denaturation method. DNA-DNA hybridization values between strain Y69^T and the closely related species were lower than 70%. Based on the data presented in this study, strain Y69^T represents a novel species for which the name Halorubrum salsamenti sp. nov. is proposed. The type of the strain is Y69^T (=CGMCC 1.15455^T = JCM 31270^T).

Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes

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.

Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34

Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

Halorubrum yunnanense sp. nov., isolated from a subterranean salt mine

Two halophilic archaeal strains, Q85T and Q86, were isolated from a subterranean salt mine in Yunnan, China. Cells were rod-shaped, Gram-stain-negative and motile. Colonies were red, smooth, convex and round (1.0–2.0 mm in diameter). The orthologous 16S rRNA and rpoB′ gene sequences of these two strains were almost identical (99.5 and 99.7 % similarities). Their closest relatives were Halorubrum kocurii BG-1T (98.0–98.1 % 16S rRNA gene sequence similarity), Halorubrum aidingense 31-hongT (97.6–97.7 %) and Halorubrum lipolyticum 9-3T (97.5–97.6 %). The level of DNA–DNA relatedness between strains Q85T and Q86 was 90 %, while that between Q85T and other related Halorubrum strains was less than 30 % (29 % for H. kocurii BG-1T, 25 % for H. aidingense 31-hongT and 22 % for H. lipolyticum 9-3T). Optimal growth of the two novel strains was observed with 20 % (w/v) NaCl and at 42–45 °C under aerobic conditions, with a slight difference in optimum Mg2+ concentration (0.7 M for Q85T, 0.5 M for Q86) and a notable difference in optimum pH (pH 7.5 for Q85T, pH 6.6 for Q86). Anaerobic growth occurred with nitrate, but not with l-arginine or DMSO. The major polar lipids of the two strains were identical, including phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated diglycosyl diether, which are the major lipids of the genus Halorubrum. The G+C contents of strains Q85T and Q86 were 66.3 and 66.8 %, respectively. Based on the phenotypic, chemotaxonomic and phylogenetic properties of strains Q85T and Q86, a novel species, Halorubrum yunnanense sp. nov., is proposed. The type strain is Q85T ( = CGMCC 1.15057T = JCM 30665T).

Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake

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).

Halorubrum rutilum sp. nov. isolated from a marine solar saltern

A halophilic archaeal strain, YJ-18-S1(T), was isolated from Yangjiang marine solar saltern, Guangxi Province, China. Cells were pleomorphic, stained Gram-negative and formed red-pigmented colonies on agar plates. Strain YJ-18-S1(T) was able to grow at 20-55 °C (optimum 37 °C), at 0.9-4.8 M NaCl (optimum 2.6 M NaCl), at 0.005-1.0 M MgCl2 (optimum 0.3 MgCl2) and at pH 5.5-8.5 (optimum pH 7.0). The cells were lysed in distilled water, and the minimal NaCl concentration to prevent cell lysis was found to be 5 % (w/v). The major polar lipids of the strain were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and sulfated mannosyl glucosyl diether. The 16S rRNA gene and rpoB' gene of strain YJ-18-S1(T) were phylogenetically related to the corresponding genes of Halorubrum members (94.3-98.0 and 86.7-96.1 % similarities, respectively). The DNA G+C content of strain YJ-18-S1(T) was 66.2 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YJ-18-S1(T) (=CGMCC 1.12554(T) = JCM 30030(T)) represents a new species of Halorubrum, for which the name Halorubrum rutilum sp. nov. is proposed.

Draft Genome Sequence of a Halorubrum H3 Strain Isolated from the Burlinskoye Salt Lake (Altai Krai, Russia)

A Halorubrum H3 strain was isolated from a water and silt sample from Burlinskoye Lake (Altai Krai, Russia, 53°8′19″N 78°24′27″E). According to 16S rRNA sequences, this strain is most closely related to Halorubrum saccharovorum. The completely sequenced and annotated genome is 3,282,373 bp and contains 3,237 genes.

Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake

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).

Halorubrum laminariae sp. nov., isolated from the brine of salted brown alga Laminaria

Two halophilic archaeal strains, R60(T) and R61, were isolated from the brine of salted brown alga Laminaria. Cells of the two strains were observed to be rod-shaped, stain Gram-negative and to lyse in distilled water. Strain R60(T) was found to contain gas vacuoles and to produce pink-pigmented colonies, while strain R61 lacked gas vacuoles and produces red-pigmented colonies. Both strains were found to be able to grow at 20-50 °C (optimum 30 °C), at 1.7-4.8 M NaCl (optimum 2.6-3.1 M NaCl), at 0-1.0 M MgCl2 (optimum 0.005-0.1 M MgCl2) and at pH 6.0-9.5 (optimum pH 7.0). The major polar lipids were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to a sulfated mannosyl glucosyl diether produced by Halorubrum members of the Halobacteriaceae. The 16S rRNA gene sequences of the two strains were 99.9 % identical, showing 94.6-98.0 % similarity to those of members of the genus Halorubrum. The EF-2 gene similarity between strains R60(T) and R60 was 100 % and showed 84.6-94.5 % similarity to those of members of the genus Halorubrum. The DNA G+C contents of the two strains were determined to be 63.0 mol %. The DNA-DNA hybridization value between strain R60(T) and strain R61 was 92 % and the two strains showed low DNA-DNA relatedness with the most related members of Halorubrum. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain R60(T) (= CGMCC 1.12689(T) = JCM 30040(T)) and strain R61 (= CGMCC 1.12696) represent a novel species of the genus Halorubrum, for which the name Halorubrum laminariae sp. nov. is proposed.

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.

Draft genome sequence of Halorubrum halophilum B8(T), an extremely halophilic archaeon isolated from salt-fermented seafood

The extremely halophilic archaeon, Halorubrum halophilum B8(T) (=JCM 18963(T), CECT 8278(T)) was isolated from salt-fermented seafood. We report here the draft genome of H. halophilum B8(T), containing 3,677,984bp with a G+C content of 65.1%. The genome consists of 19 genes predicted to encode esterases.

Draft Genome Sequence of the Polyextremophilic Halorubrum sp. Strain AJ67, Isolated from Hyperarsenic Lakes in the Argentinian Puna

Halorubrum sp. strain AJ67, an extreme halophilic UV-resistant archaeon, was isolated from Laguna Antofalla in the Argentinian Puna. The draft genome sequence suggests the presence of potent enzyme candidates that are essential for survival under multiple environmental extreme conditions, such as high UV radiation, elevated salinity, and the presence of critical arsenic concentrations.

Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood

A novel, red-pigmented, pleomorphic and short rod-shaped haloarchaeon, designated B8(T), was isolated from a salt-fermented seafood. Strain B8(T) was found to be able to grow at 20-45 °C, in the presence of 15-30 % (w/v) NaCl and at pH 7.0-9.0. The optimum requirements were found to be a temperature range of 35-40 °C, pH 8.0 and the presence of 25 % NaCl. The cells of strain B8(T) were observed to be Gram-staining negative and lysed in distilled water. Anaerobic growth did not occur in the presence of nitrate, L-arginine, dimethyl sulfoxide or trimethylamine N-oxide. The catalase and oxidase activities were found to be positive and nitrate was reduced in aerobic conditions. Tween 20, 40 and 80 were found to be hydrolyzed, whereas casein, gelatin and starch were not hydrolyzed. Indole or H2S was not formed and urease activity was not detected. A phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain B8(T) is most closely related to members of the genus Halorubrum in the family Halobacteriaceae. Strain B8(T) was found to have three 16S rRNA genes, rrnA, rrnB and rrnC; similarities between the 16S rRNA gene sequences are 99.0-99.8 %. Strain B8(T) shared 99.0 % 16S rRNA gene sequence similarity with Halorubrum (Hrr.) lipolyticum JCM 13559(T) and Hrr. saccharovorum DSM 1137(T), 98.8 % with Hrr. kocurii JCM 14978(T), 98.3 % with Hrr. lacusprofundi DSM 5036(T), 98.0 % with Hrr. arcis JCM 13916(T), 97.7 % with Hrr. aidingense JCM 13560(T) and 97.0 % with Hrr. aquaticum JCM 14031(T), as well as 93.7-96.5 % with other type strains in the genus Halorubrum. The RNA polymerase subunit B' gene sequence similarity of strain B8(T) with Hrr. kocurii JCM 14978(T) is 97.2 % and lower with other members of the genus Halorubrum. DNA-DNA hybridization experiments showed that strain B8(T) shared equal or lower than 50 % relatedness with reference species in the genus Halorubrum. The genomic DNA G+C content of strain B8(T) was determined to be 64.6 mol%. The major isoprenoid quinone of strain B8(T) was identified as menaquinone-8 and the major polar lipids as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and an unidentified phospholipid. Based on this polyphasic taxonomic study, strain B8(T) is considered to represent a new species in the genus Halorubrum, for which the name Hrr. halophilum sp. nov. is proposed. The type strain is B8(T) (=JCM 18963(T) = CECT 8278(T)).

Halorubrum rubrum sp. nov., an extremely halophilic archaeon from a Chinese salt lake

Two halophilic archaeal strains, YC87(T) and YCA11, were isolated from Yuncheng salt lake in Shanxi, China. Cells of the two strains were observed to be pleomorphic rod-shaped, stained Gram-negative and produced red-pigmented colonies. Strain YC87(T) was able to grow at 20-50 °C (optimum 37 °C), at 1.4-4.8 M NaCl (optimum 2.1 M NaCl), at 0.05-1.0 M MgCl2 (optimum 0.3 M MgCl2) and at pH 6.0-9.0 (optimum pH 7.0) while strain YCA11 was able to grow at 20-50 °C (optimum 37 °C), at 2.1-4.8 M NaCl (optimum 3.1 M NaCl), at 0.01-0.7 M MgCl2 (optimum 0.1 M MgCl2) and at pH 6.0-9.0 (optimum pH 7.5). The cells of both isolates were observed to lyse in distilled water. The minimum NaCl concentrations that prevented cell lysis were determined to be 8 % (w/v) for strain YC87(T) and 12 % (w/v) for strain YCA11. The major polar lipids of the two strains were identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether; another major glycolipid and trace amounts of several unidentified lipids were also detected. The 16S rRNA gene sequences of the two strains were 99.8 % identical, showing 93.2-98.2 % similarity to members of the genus Halorubrum of the family Halobacteriaceae. The rpoB' gene similarity between strains YC87(T) and YCA11 was 99.3 % and showed 87.5-95.2 % similarity to the closest relative members of the genus Halorubrum. The DNA G+C content of strains YC87(T) and YCA11 were determined to be 64.9 and 64.5 mol%, respectively. The DNA-DNA hybridization value between strain YC20(T) and strain YC77 was 87 % and the two strains showed low DNA-DNA relatedness with Halorubrum cibi JCM 15757(T) and Halorubrum aquaticum CGMCC 1.6377(T), the most related members of the genus Halorubrum. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strains YC87(T) and YCA11 represent a novel species of the genus Halorubrum, for which the name Halorubrum rubrum sp. nov. is proposed. The type strain is YC87(T) (=CGMCC 1.12124(T) = JCM 18365(T)).

Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics

The halophilic Archaea of the family Halobacteriaceae (36 genera with 129 species with standing in nomenclature as of November 2011) provide an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods have influenced the way in which the taxonomy of a single group of prokaryotes is treated. This review gives an overview of the taxonomy of the family Halobacteriaceae, showing the impact that methods of phenotypic characterization, numerical taxonomy, chemotaxonomy and especially polar lipid analysis, 16S rRNA gene sequence comparisons, multilocus type analysis and comparative genomics have had on their classification.

Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia

An extremely halophilic archaeon, strain ETD6, was isolated from a marine solar saltern in Sfax, Tunisia. Analysis of the 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genus Halorubrum among the family Halobacteriaceae, with a close relationship to Hrr. xinjiangense (99.77% of identity). However, value for DNA-DNA hybridization between strain ETD6 and Hrr.xinjiangense were about 24.5%. The G+C content of the genomic DNA was 65.1 mol% (T(m)). Strain ETD6 grew in 15-35% (w/v) NaCl. The temperature and pH ranges for growth were 20-55°C and 6-9, respectively. Optimal growth occurred at 25% NaCl, 37°C, and pH 7.4. The results of the DNA hybridization against Hrr. xinjiangense and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain ETD6 from other Hrr. species. Therefore, strain ETD6 represents a novel species of the genus Halorubrum, for which the name Hrr. sfaxense sp. nov. is proposed. The Genbank EMBL-EBI accession number is GU724599.

Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes

Two halophilic archaea, strains EN-2T and SH-4, were isolated from the saline lakes Erliannor and Shangmatala, respectively, in Inner Mongolia, China. Cells were strictly aerobic, motile rods. Colonies were red. Strains EN-2T and SH-4 were able to grow at 25–50 °C (optimum 35–40 °C), with 2.5–5.0 M NaCl (optimum 3.4 M NaCl) and at pH 6.0–9.0 (optimum pH 7.5). MgCl2 was not required for growth. Cells lysed in distilled water and the lowest NaCl concentration that prevented cell lysis was 12 % (w/v). On the basis of 16S rRNA gene sequence analysis, strains EN-2T and SH-4 were closely related to Halorubrum cibi B31T (97.9 and 98.0 % similarity, respectively), Hrr. tibetense 8W8T (97.3 and 97.7 %), Hrr. alkaliphilum DZ-1T (96.8 and 97.1 %), Hrr. luteum CGSA15T (96.8 and 97.0 %) and Hrr. lipolyticum 9-3T (96.8 and 97.0 %). DNA–DNA hybridization showed that strains EN-2T and SH-4 did not belong to the same species as any of these strains (≤45 % DNA–DNA relatedness) but that they are members of the same species (>70 % DNA–DNA relatedness). Polar lipid analysis revealed that strains EN-2T and SH-4 contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated diglycosyl diethers and several unidentified glycolipids. The DNA G+C content of both isolates was 62.1 mol%. It was concluded that strains EN-2T and SH-4 represent a novel species of the genus Halorubrum, for which the name Halorubrum aquaticum sp. nov. is proposed. The type strain is EN-2T ( = CECT 7174T  = CGMCC 1.6377T  = JCM 14031T).

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).

Metagenomics and recovery of enzyme genes from alkaline saline environments

Enzymes functioning at alkaline pH are widely used in the detergent industry as additives to improve the stain removal properties of domestic and industrial cleaning products. This industry provides by far the major mass market for enzymes. With constantly changing formulations in detergents and concerns over energy demands, new and improved enzymes are constantly in demand. Soda lakes host dense populations of alkali-loving microbes and, as such, provide vast reservoirs of potentially useful enzymes for such an industry. Traditional recovery methods for new enzymes have involved the isolation of microbes, preferably from a compatible chemical environment such as a soda lake, followed by screening of the isolates for useful enzymic activity. At least two commercially significant enzymes originating from soda lake microbes have been marketed following this route. However, the failure to cultivate more than a small percentage of microbes from most environments necessarily markedly reduces the recovery of new enzymes. In recent years, interest has focussed on more comprehensive recovery methods based around detecting appropriate enzyme genes in nucleic acids extracted from potentially useful sites, thus maximizing coverage of the whole genetic resource in a particular biotope. Here we review progress to date in soda lake biotopes and discuss ways the field may develop in the future.

Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species

Polyhydroxyalkanoates (PHAs) are accumulated in many prokaryotes. Several members of the Halobacteriaceae produce poly-3-hydroxybutyrate (PHB), but it is not known if this is a general property of the family. We evaluated identification methods for PHAs with 20 haloarchaeal species, three of them isolates from Permian salt. Staining with Sudan Black B, Nile Blue A, or Nile Red was applied to screen for the presence of PHAs. Transmission electron microscopy and (1)H-nuclear magnetic resonance spectroscopy were used for visualization of PHB granules and chemical confirmation of PHAs in cell extracts, respectively. We report for the first time the production of PHAs by Halococcus sp. (Halococcus morrhuae DSM 1307(T), Halococcus saccharolyticus DSM 5350(T), Halococcus salifodinae DSM 8989(T), Halococcus dombrowskii DSM 14522(T), Halococcus hamelinensis JCM 12892(T), Halococcus qingdaonensis JCM 13587(T)), Halorubrum sp. (Hrr. coriense DSM 10284(T), Halorubrum chaoviator DSM 19316(T), Hrr. chaoviator strains NaxosII and AUS-1), haloalkaliphiles (Natronobacterium gregoryi NCMB 2189(T), Natronococcus occultus DSM 3396(T)) and Halobacterium noricense DSM 9758(T). No PHB was detected in Halobacterium salinarum NRC-1 ATCC 700922, Hbt. salinarum R1 and Haloferax volcanii DSM 3757(T). Most species synthesized PHAs when growing in synthetic as well as in complex medium. The polyesters were generally composed of PHB and poly-ss-hydroxybutyrate-co-3-hydroxyvalerate (PHBV). Available genomic data suggest the absence of PHA synthesis in some haloarchaea and in all other Euryarchaeota and Crenarchaeota. Homologies between haloarchaeal and bacterial PHA synthesizing enzymes had indicated to some authors probable horizontal gene transfer, which, considering the data obtained in this study, may have occurred already before Permian times.

The single-stranded DNA genome of novel archaeal virus halorubrum pleomorphic virus 1 is enclosed in the envelope decorated with glycoprotein spikes

Only a few archaeal viruses have been subjected to detailed structural analyses. Major obstacles have been the extreme conditions such as high salinity or temperature needed for the propagation of these viruses. In addition, unusual morphotypes of many archaeal viruses have made it difficult to obtain further information on virion architectures. We used controlled virion dissociation to reveal the structural organization of Halorubrum pleomorphic virus 1 (HRPV-1) infecting an extremely halophilic archaeal host. The single-stranded DNA genome is enclosed in a pleomorphic membrane vesicle without detected nucleoproteins. VP4, the larger major structural protein of HRPV-1, forms glycosylated spikes on the virion surface and VP3, the smaller major structural protein, resides on the inner surface of the membrane vesicle. Together, these proteins organize the structure of the membrane vesicle. Quantitative lipid comparison of HRPV-1 and its host Halorubrum sp. revealed that HRPV-1 acquires lipids nonselectively from the host cell membrane, which is typical of pleomorphic enveloped viruses.

Archaeosomes made of Halorubrum tebenquichense total polar lipids: a new source of adjuvancy

Background

Archaeosomes (ARC), vesicles prepared from total polar lipids (TPL) extracted from selected genera and species from the Archaea domain, elicit both antibody and cell-mediated immunity to the entrapped antigen, as well as efficient cross priming of exogenous antigens, evoking a profound memory response. Screening for unexplored Archaea genus as new sources of adjuvancy, here we report the presence of two new Halorubrum tebenquichense strains isolated from grey crystals (GC) and black mood (BM) strata from a littoral Argentinean Patagonia salt flat. Cytotoxicity, intracellular transit and immune response induced by two subcutaneous (sc) administrations (days 0 and 21) with BSA entrapped in ARC made of TPL either form BM (ARC-BM) and from GC (ARC-GC) at 2% w/w (BSA/lipids), to C3H/HeN mice (25 μg BSA, 1.3 mg of archaeal lipids per mouse) and boosted on day 180 with 25 μg of bare BSA, were determined.

Results

DNA G+C content (59.5 and 61.7% mol BM and GC, respectively), 16S rDNA sequentiation, DNA-DNA hybridization, arbitrarily primed fingerprint assay and biochemical data confirmed that BM and GC isolates were two non-previously described strains of H. tebenquichense. Both multilamellar ARC mean size were 564 ± 22 nm, with -50 mV zeta-potential, and were not cytotoxic on Vero cells up to 1 mg/ml and up to 0.1 mg/ml of lipids on J-774 macrophages (XTT method). ARC inner aqueous content remained inside the phago-lysosomal system of J-774 cells beyond the first incubation hour at 37°C, as revealed by pyranine loaded in ARC. Upon subcutaneous immunization of C3H/HeN mice, BSA entrapped in ARC-BM or ARC-GC elicited a strong and sustained primary antibody response, as well as improved specific humoral immunity after boosting with the bare antigen. Both IgG1 and IgG2a enhanced antibody titers could be demonstrated in long-term (200 days) recall suggesting induction of a mixed Th1/Th2 response.

Conclusion

We herein report the finding of new H. tebenquichense non alkaliphilic strains in Argentinean Patagonia together with the adjuvant properties of ARC after sc administration in mice. Our results indicate that archaeosomes prepared with TPL from these two strains could be successfully used as vaccine delivery vehicles.

Halorubrum chaoviator sp. nov., a haloarchaeon isolated from sea salt in Baja California, Mexico, Western Australia and Naxos, Greece

Three halophilic isolates, strains Halo-G*T, AUS-1 and Naxos II, were compared. Halo-G* was isolated from an evaporitic salt crystal from Baja California, Mexico, whereas AUS-1 and Naxos II were isolated from salt pools in Western Australia and the Greek island of Naxos, respectively. Halo-G*T had been exposed previously to conditions of outer space and survived 2 weeks on the Biopan facility. Chemotaxonomic and molecular comparisons suggested high similarity between the three strains. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strains clustered with Halorubrum species, showing sequence similarities of 99.2-97.1%. The DNA-DNA hybridization values of strain Halo-G*T and strains AUS-1 and Naxos II are 73 and 75%, respectively, indicating that they constitute a single species. The DNA relatedness between strain Halo-G*T and the type strains of 13 closely related species of the genus Halorubrum ranged from 39 to 2%, suggesting that the three isolates constitute a different genospecies. The G+C content of the DNA of the three strains was 65.5-66.5 mol%. All three strains contained C20C20 derivatives of diethers of phosphatidylglycerol, phosphatidylglyceromethylphosphate and phosphatidylglycerolsulfate, together with a sulfated glycolipid. On the basis of these results, a novel species that includes the three strains is proposed, with the name Halorubrum chaoviator sp. nov. The type strain is strain Halo-G*T (=DSM 19316T=NCIMB 14426T=ATCC BAA-1602T).

Isolation and characterization of halophilic Archaea able to produce biosurfactants

Halotolerant microorganisms able to live in saline environments offer a multitude of actual or potential applications in various fields of biotechnology. This is why some strains of Halobacteria from an Algerian culture collection were screened for biosurfactant production in a standard medium using the qualitative drop-collapse test and emulsification activity assay. Five of the Halobacteria strains reduced the growth medium surface tension below 40 mN m(-1), and two of them exhibited high emulsion-stabilizing capacity. Diesel oil-in-water emulsions were stabilized over a broad range of conditions, from pH 2 to 11, with up to 35% sodium chloride or up to 25% ethanol in the aqueous phase. Emulsions were stable to three cycles of freezing and thawing. The components of the biosurfactant were determined; it contained sugar, protein and lipid. The two Halobacteria strains with enhanced biosurfactant producers, designated strain A21 and strain D21, were selected to identify by phenotypic, biochemical characteristics and by partial 16S rRNA gene sequencing. The strains have Mg(2+), and salt growth requirements are always above 15% (w/v) salts with an optimal concentration of 15-25%. Analyses of partial 16S rRNA gene sequences of the two strains suggested that they were halophiles belonging to genera of the family Halobacteriaceae, Halovivax (strain A21) and Haloarcula (strain D21). To our knowledge, this is the first report of biosurfactant production at such a high salt concentration.