Publications

halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes.	two halophilic archaea, strains en-2(t) 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-2(t) 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). mgcl(2) was not required for growth. cells lysed in distilled water and the lowest nacl concentration that prevented cell lysis was 12 ...	2011	20543150
characterization of heterotrophic prokaryote subgroups in the sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis.	here, we combined flow cytometry (fcm) and phylogenetic analyses after cell sorting to characterize the dominant groups of the prokaryotic assemblages inhabiting two ponds of increasing salinity: a crystallizer pond (ts) with a salinity of 390 g/l, and the non-crystallizer pond (m1) with a salinity of 200 g/l retrieved from the solar saltern of sfax in tunisia. as expected, fcm analysis enabled the resolution of high nucleic acid content (hna) and low nucleic acid content (lna) prokaryotes. next ...	2011	21424516
a high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex.	technologies for silencing the electrical activity of genetically targeted neurons in the brain are important for assessing the contribution of specific cell types and pathways toward behaviors and pathologies. recently we found that archaerhodopsin-3 from halorubrum sodomense (arch), a light-driven outward proton pump, when genetically expressed in neurons, enables them to be powerfully, transiently, and repeatedly silenced in response to pulses of light. because of the impressive characteristi ...	2011	21811444
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 ...	2011	21754938
Halopenitus persicus gen. nov., sp. nov., a novel archaeon from an inland salt lake in Iran.	A novel pale pink-pigmented halophilic archaeon, strain DC30T, was isolated from Aran-Bidgol salt lake, a hypersaline playa in Iran. The cells of strain DC30T were nonmotile and pleomorphic, from rods to triangular or disk shaped. Strain DC30T needs at least 1.7 M NaCl and 0.05 M MgCl2 for growth. Optimal growth was achieved at 3 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.5 and 40 °C, respectively, while it was able to grow over pH and temperature ranges of 6.5- ...	2011	22003044
phylogenetic diversities and community structure of members of the extremely halophilic archaea (order halobacteriales) in multiple saline sediment habitats.	we investigated the phylogenetic diversity and community structure of members of the halophilic archaea (order halobacteriales) in five distinct sediment habitats that experience various levels of salinity and salinity fluctuations (sediments from great salt plains, and zodletone spring in oklahoma, mangrove tree sediments in puerto rico, sediment underneath salt heaps in a salt-processing plant, and sediments from the great salt lake northern arm) using halobacteriales-specific 16s rrna gene pr ...	2011	22179255
prokaryotic diversity in aran-bidgol salt lake, the largest hypersaline playa in iran.	prokaryotic diversity in aran-bidgol salt lake, a thalasohaline lake in iran, was studied by fluorescence in situ hybridization (fish), cultivation techniques, denaturing gradient gel electrophoresis (dgge) of pcr-amplified fragments of 16s rrna genes and 16s rrna gene clone library analysis. viable counts obtained (2.5-4×10(6) cells ml(-1)) were similar to total cell abundance in the lake determined by dapi direct count (3-4×10(7) cells ml(-1)). the proportion of bacteria to archaea in the comm ...	2011	22185719
survival of extremely and moderately halophilic isolates of tunisian solar salterns after uv-b or oxidative stress.	adaptation to a solar saltern environment requires mechanisms providing tolerance not only to salinity but also to uv radiation (uvr) and to reactive oxygen species (ros). we cultivated prokaryote halophiles from two different salinity ponds: the concentrator m1 pond (240 g·l(-1) nacl) and the crystallizer ts pond (380 g·l(-1) nacl). we then estimated uv-b and hydrogen peroxide resistance according to the optimal salt concentration for growth of the isolates. we observed a higher biodiversity of ...	2011	22017705
Optical recording of action potentials in mammalian neurons using a microbial rhodopsin.	Reliable optical detection of single action potentials in mammalian neurons has been one of the longest-standing challenges in neuroscience. Here we achieved this goal by using the endogenous fluorescence of a microbial rhodopsin protein, Archaerhodopsin 3 (Arch) from Halorubrum sodomense, expressed in cultured rat hippocampal neurons. This genetically encoded voltage indicator exhibited an approximately tenfold improvement in sensitivity and speed over existing protein-based voltage indicators, ...	2011	22120467
diversity of virus-host systems in hypersaline lake retba, senegal.	summary remarkable morphological diversity of virus-like particles was observed by transmission electron microscopy in a hypersaline water sample from lake retba, senegal. the majority of particles morphologically resembled hyperthermophilic archaeal dna viruses isolated from extreme geothermal environments. some hypersaline viral morphotypes have not been previously observed in nature, and less than 1% of observed particles had a head-and-tail morphology, which is typical for bacterial dna viru ...	2010	20738373
biodiversity of archaea and floral of two inland saltern ecosystems in the alto vinalopó valley, spain.	abstract:	2010	20942947
culture-independent study of the diversity of microbial populations in brines during fermentation of naturally-fermented aloreña green table olives.	aloreña table olives are naturally fermented traditional green olives with a denomination of protection (dop). the present study focused on aloreña table olives manufactured by small and medium enterprises (smes) from valle del guadalhorce (southern spain) under three different conditions (cold storage, and ambient temperature fermentations in small vats and in large fermentation tanks). the microbial load of brines during fermentation was studied by plate counting, and the microbial diversity w ...	2010	21122933
new, closely related haloarchaeal viral elements with different nucleic acid types.	during the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus, haloarcula hispanica pleomorphic virus 1 (hhpv-1), that infects the halophilic archaeon haloarcula hispanica. the virus contains a circular double-stranded dna genome of 8,082 bp in size. the organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus hrpv-1, a pleomorphic single-stranded dna virus tha ...	2010	20089654
diversity of haloquadratum and other haloarchaea in three, geographically distant, australian saltern crystallizer ponds.	haloquadratum walsbyi is frequently a dominant member of the microbial communities in hypersaline waters. 16s rrna gene sequences indicate that divergence within this species is very low but relatively few sites have been examined, particularly in the southern hemisphere. the diversity of haloquadratum was examined in three coastal, but geographically distant saltern crystallizer ponds in australia, using both culture-independent and culture-dependent methods. two 97%-otu, comprising haloquadrat ...	2010	20091074
tantalizing evidence for caspase-like protein expression and activity in the cellular stress response of archaea.	an enigmatic feature of microbial evolution is the emergence of programmed cell death (pcd), a genetically controlled form of cell suicide triggered by environmental stimuli. archaea, the second major prokaryotic domain of life, have been notably absent from the pcd inheritance discussion, due to a lack of genetic homologues. using the model haloarchaeon haloferax volcanii, we document extremely high caspase-specific activity and expression of immunoreactive proteins to human caspase 8 antisera, ...	2010	20132282
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 spe ...	2010	20437233
halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer.	strains 1.15.5(t), 2.27.5, 5.24.4 and 6.14.5 were isolated from a solar saltern. they have flattened, rod-shaped cells and are aerobic, extremely halophilic members of the domain archaea and family halobacteriaceae. cells stained gram-negative and grew optimally in media around neutral ph and containing 20-24 % (w/v) (strains 1.15.5(t) and 2.27.5) or 22-24 % (w/v) (5.24.4 and 6.14.5) salts. mg(2+) was not required. the dna g+c contents of these isolates were all close to 58 mol%, and dna-dna cro ...	2010	19667389
archaeal diversity in the haloalkaline lake elmenteita in kenya.	a non-culture approach was used to study the archaeal diversity in lake elmenteita, kenya. five different sampling points were selected randomly within the lake. wet sediments and water samples were collected from each sampling point. in addition, dry mud cake was collected from three points where the lake had dried. dna was extracted from these samples and the 16s rrna genes were amplified using primers described to be domain-specific for archaea. eleven clone libraries were constructed using p ...	2010	19806396
halophilic archaea cultured from ancient halite, death valley, california.	halophilic archaea cultured from ancient fluid inclusions in a 90-m-long (0- to 100,000-year-old) salt core from death valley, california, demonstrate survival of bacterial cells in subsurface halite for up to 34,000 years. five enrichment cultures, representing three genera of halophilic archaea (halorubrum, natronomonas and haloterrigena), were obtained from five surface-sterilized halite crystals exclusively in one section of the core (13.0-17.8 m; 22,000-34,000 years old) containing perennia ...	2010	19840101
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 halophili ...	2010	19864380
high-performance genetically targetable optical neural silencing by light-driven proton pumps.	the ability to silence the activity of genetically specified neurons in a temporally precise fashion would provide the opportunity to investigate the causal role of specific cell classes in neural computations, behaviours and pathologies. here we show that members of the class of light-driven outward proton pumps can mediate powerful, safe, multiple-colour silencing of neural activity. the gene archaerhodopsin-3 (arch) from halorubrum sodomense enables near-100% silencing of neurons in the awake ...	2010	20054397
studies on the biodiversity of halophilic microorganisms isolated from el-djerid salt lake (tunisia) under aerobic conditions.	bacterial and archaeal aerobic communities were recovered from sediments from the shallow el-djerid salt lake in tunisia, and their salinity gradient distribution was established. six samples for physicochemical and microbiological analyses were obtained from 6 saline sites in the lake for physico-chemical and microbiological analyses. all samples studied were considered hypersaline with nacl concentration ranging from 150 to 260 g/l. a specific halophilic microbial community was recovered from ...	2009	20066169
haloarchaeal diversity in 23, 121 and 419 mya salts.	dna was extracted from surface-sterilized salt of different geological ages (23, 121, 419 million years of age, mya) to investigate haloarchaeal diversity. only haloarcula and halorubrum dna was found in 23 mya salt. older crystals contained unclassified groups and halobacterium. the older crystals yielded a unique 55-bp insert within the 16s rrna v2 region. the secondary structure of the v2 region completely differed from that in haloarchaea of modern environments. the dna demonstrates that unk ...	2009	19849725
archaeosomes made of halorubrum tebenquichense total polar lipids: a new source of adjuvancy.	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) st ...	2009	19678953
tryptophan inhibits bacteriorhodopsin formation in halorubrum sodomense a01.	bacteriorhodopsin (br) is well recognized for its applied values. we observed that the bottleneck associated with the use of different peptones for br production was linked to the presence of tryptophan (trp). trp at 0.36 mm in the culture medium inhibits br formation. the results obtained in this study demonstrate that br content (mg l(-1)) of halorubrum sodomense a01 decreased to 2.9 mg l(-1) in 0.36 mm trp compared to control (0.11 mm trp) where 12.3 mg l(-1) of br was obtained. our results p ...	2009	19025874
characterization of salicola sp. ic10, a lipase- and protease-producing extreme halophile.	in order to explore the diversity of extreme halophiles able to produce different hydrolytic enzymes (amylase, protease, lipase and dnase) in hypersaline habitats of south spain, a screening program was performed. a total of 43 extreme halophiles showing hydrolytic activities have been isolated and characterized. the isolated strains were able to grow optimally in media with 15-20% (w/v) total salts and in most cases, growth was detected up to 30% (w/v) total salts. most hydrolase producers were ...	2009	19187212
emended descriptions of genera of the family halobacteriaceae.	the family halobacteriaceae currently contains 96 species whose names have been validly published, classified in 27 genera (as of september 2008). in recent years, many novel species have been added to the established genera but, in many cases, one or more properties of the novel species do not agree with the published descriptions of the genera. authors have often failed to provide emended genus descriptions when necessary. following discussions of the international committee on systematics of ...	2009	19244452
a critique of prokaryotic species concepts.	developments in dna sequencing and population genetics analyses have revealed unanticipated complexity in prokaryotic variation. the observation that genetic traits are horizontally inherited at unexpected rates within and between closely related asexually reproducing lineages impacts our comprehension of prokaryotic evolution and ecology. as a result, the concepts that point to species as being discrete clusters or monophyletic lineages are at odds with most of the data, suggesting that taxon c ...	2009	19271197
an ssdna virus infecting archaea: a new lineage of viruses with a membrane envelope.	archaeal organisms are generally known as diverse extremophiles, but they play a crucial role also in moderate environments. so far, only about 50 archaeal viruses have been described in some detail. despite this, unusual viral morphotypes within this group have been reported. interestingly, all isolated archaeal viruses have a double-stranded dna (dsdna) genome. to further characterize the diversity of archaeal viruses, we screened highly saline water samples for archaea and their viruses. here ...	2009	19298373
archaeal diversity at the great salt plains of oklahoma described by cultivation and molecular analyses.	the great salt plains of oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly nacl. previous work described the bacterial community through the characterization of 105 isolates from 46 phylotypes. the current report describes the archaeal community through both microbial isolation and culture-independent techniques. nineteen distinct archaea were isolated, and ten were characterized phenetically. included were isolates phylogenetically related to ...	2009	19306116
halorubrum cibi sp. nov., an extremely halophilic archaeon from salt-fermented seafood.	strain b31(t) is a gram-staining-negative, motile, and extremely halophilic archaeon that was isolated from salt-fermented seafood. its morphology, physiology, biochemical features, and 16s rrna gene sequence were determined. phylogenetic analysis of its 16s rrna gene sequence and composition of its major polar lipids placed this archaeon in the genus halorubrum of the family halobacteriaceae. strain b31(t) showed 97.3, 97.2, and 96.9 % 16s rrna similarity to the type strains of halorubrum alkal ...	2009	19412599
characterization of halophiles isolated from solar salterns in baja california, mexico.	solar salterns are extreme hypersaline environments that are five to ten times saltier than seawater (150-300 g l(-1) salt concentration) and typically contain high numbers of halophiles adapted to tolerate such extreme hypersalinity. thirty-five halophile cultures of both bacteria and archaea were isolated from the exportadora de sal saltworks in guerrero negro, baja california, mexico. 16s rrna sequence analysis showed that these cultured isolates included members belonging to the halorubrum, ...	2009	19418017
halorubrum chaoviator sp. nov., a haloarchaeon isolated from sea salt in baja california, mexico, western australia and naxos, greece.	three halophilic isolates, strains halo-gt, 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. phylogene ...	2009	19567575
structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2.	archaerhodopsin-2 (ar2), a retinal protein-carotenoid complex found in the claret membrane of halorubrum sp. aus-2, functions as a light-driven proton pump. in this study, the membrane fusion method was utilized to prepare trigonal p321 crystals (a=b=98.2 a, c=56.2 a) and hexagonal p6(3) crystals (a=b=108.8 a, c=220.7 a). the trigonal crystal is made up of stacked membranes in which the ar2 trimers are arranged on a honeycomb lattice. similar membranous structures are found in the hexagonal crys ...	2008	18082767
halorubrum luteum sp. nov., isolated from lake chagannor, inner mongolia, china.	a novel halophilic archaeon, strain cgsa15(t), was isolated from water of lake chagannor in china. the strain grew optimally at 33-37 degrees c, ph 9.5-10.0 and 4.0-4.3 m nacl. the major polar lipids were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. the genomic dna g+c content of strain cgsa15(t) was 60.2 mol%. phylogenetic analysis based on 16s rrna gene sequences revealed that strain cgsa15(t) was a member of the genus halorubrum and was related most closely to halorub ...	2008	18599720
halorubrum kocurii sp. nov., an archaeon isolated from a saline lake.	a gram-negative, non-motile, neutrophilic, rod-shaped, extremely halophilic archaeon, designated strain bg-1(t), was isolated from a salt lake, lake bagaejinnor, in inner mongolia, china. strain bg-1(t) was able to grow at 25-55 degrees c, required at least 2.5 m nacl for growth (with an optimum at 3.4 m nacl) and grew at ph 6.0-9.0 (with an optimum at ph 7.5). hypotonic treatment with less than 2.0 m nacl caused cell lysis. phylogenetic analysis of the almost-complete 16s rrna gene sequence pos ...	2008	18768599
halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in california, usa.	a motile, rod-shaped, pink-pigmented, extremely halophilic archaeon, strain sf3-213(t), was isolated from a crystallizer pond at the cargill solar salt plant, newark, california (usa). analysis of the almost-complete 16s rrna gene sequence showed that the isolate was phylogenetically related to species of the genus halorubrum, with a close relationship to halorubrum trapanicum nrc 34021(t) (98.6 % similarity), halorubrum sodomense atcc 33755(t) (98.3 %) and halorubrum xinjiangense as 1.3527(t) ( ...	2008	19060045
cardiolipin is associated with the terminal oxidase of an extremely halophilic archaeon.	membranes having an a high content of cardiolipin were isolated from an extremely halophilic archaeon halorubrum sp. absorbance difference spectra of detergent-solubilized plasma membranes reduced by dithionite suggested the presence of b-type cytochromes. non-denaturing gel electrophoresis revealed only one fraction having tmpd-oxidase activity in which cardiolipin was the major lipid component. the electroeluted fraction showed a cytochrome c oxidase activity characterized by the reduced minus ...	2007	17266932
genetic analysis of a novel plasmid pzmx101 from halorubrum saccharovorum: determination of the minimal replicon and comparison with the related haloarchaeal plasmid pscm201.	the dna sequence of a novel haloarchaeal plasmid pzmx101 (3918 bp) from halorubrum saccharovorum was determined and six orfs were predicted. the largest orf encodes a putative replication initiation protein repa, which shares 40% sequence similarity with the rep201 of a theta-replication plasmid pscm201 recently isolated from haloarcula, suggesting that pzmx101 might replicate via a theta-type mechanism. using pzmx101 as the only haloarchaeal replicon, a shuttle vector pzmx108 was constructed an ...	2007	17371299
haloplanus natans gen. nov., sp. nov., an extremely halophilic, gas-vacuolate archaeon isolated from dead sea-red sea water mixtures in experimental outdoor ponds.	to study biological phenomena in the dead sea and to simulate the effects of mixing dead sea water with red sea water, experimental mesocosms were operated at the dead sea works at sedom, israel. dense communities of red halophilic archaea developed in mesocosms filled with 80 % dead sea water and 20 % red sea water after enrichment with phosphate. the most common type of colonies isolated from these brines belonged to the genus halorubrum. a few white-pinkish opaque colonies contained pleomorph ...	2007	17392206
halorubrum arcis sp. nov., an extremely halophilic archaeon isolated from a saline lake on the qinghai-tibet plateau, china.	a gram-negative, aerobic, neutrophilic and extremely halophilic archaeon (strain aj201(t)), isolated from ayakekum salt lake on the qinghai-tibet plateau, was investigated by a polyphasic approach. the dna g+c content of strain aj201(t) was 65.7 mol%. the major polar lipid profile and phylogenetic analysis based on 16s rrna gene sequences supported the allocation of the strain to the genus halorubrum. the results of dna-dna hybridizations and physiological and biochemical tests allowed genotypic ...	2007	17473261
haloarchaeal communities in the crystallizers of two adriatic solar salterns.	solar salterns operate only for short dry periods of the year in the north shore of the adriatic sea because of its relatively humid and cold mediterranean climate. in a previous paper, we showed that the nacl precipitation ponds (crystallizers) of northern adriatic secovlje salterns have different haloarchaeal populations from those typically found in dry and hot climates such as southern spain. to check whether there is a common pattern of haloarchaeal diversity in these less extreme condition ...	2007	17496945
[prokaryotic microbial diversity of the ancient salt deposits in the kunming salt mine, p.r. china].	the prokaryotic microbial diversity of the ancient salt deposits in the kunming salt mine, pr china was investigated using pcr-dgge and rrna approaches. total community dna was extracted and purified by a direct method, which yielded amplified dna of high molecular weight for samples. a variable region of 16s rrna gene was then amplified by pcr with bacterial and archaeal primers and analyzed by denaturing gradient gel electrophoresis (dgge). twenty-seven major bands were detected in the bacteri ...	2007	17552238
searching for species in haloarchaea.	prokaryotic (bacterial and archaeal) species definitions and the biological concepts that underpin them entail clustering (cohesion) among individuals, in terms of genome content and gene sequence similarity. homologous recombination can maintain gene sequence similarity within, while permitting divergence between, clusters and is thus the basis for recent efforts to apply the biological species concept in prokaryote systematics and ecology. in this study, we examine isolates of the haloarchaeal ...	2007	17715057
halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern.	an extremely halophilic archaeon, strain fa-1(t), was isolated from a marine solar saltern in fujian, china. strain fa-1(t) required mg2+ and at least 2.0 m nacl for growth. it was able to grow at ph 6.5-9.0 (optimally at ph 7.0-7.5) and at 20-55 degrees c (optimally at 37-42 degrees c). the major polar lipids of strain fa-1(t) were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl diether. on the basis of a 16s rrna gene se ...	2007	17911283
halorubrum ejinorense sp. nov., isolated from lake ejinor, inner mongolia, china.	a novel halophilic archaeon, strain ej-32t, was isolated from water from lake ejinor in inner mongolia, china. the taxonomy of strain ej-32t was studied by using a polyphasic approach. on the basis of 16s rrna gene sequence similarities, strain ej-32t was shown to be phylogenetically related to halorubrum coriense (97.9%), halorubrum trapanicum (97.9%), halorubrum sodomense (97.8%), halorubrum tebenquichense (97.8%), halorubrum xinjiangense (97.6%), halorubrum terrestre (97.4%), halorubrum distr ...	2007	17978215
sequence analysis of an archaeal virus isolated from a hypersaline lake in inner mongolia, china.	we are profoundly ignorant about the diversity of viruses that infect the domain archaea. less than 100 have been identified and described and very few of these have had their genomic sequences determined. here we report the genomic sequence of a previously undescribed archaeal virus.	2007	17996081
diversity of halophilic archaea from six hypersaline environments in turkey.	the diversity of archaeal strains from six hypersaline environments in turkey was analyzed by comparing their phenotypic characteristics and 16s rdna sequences. thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16s rdna gene sequences. the results showed that all isolates belong to the family halobacteriacea ...	2007	18050917
crystal structures of archaerhodopsin-1 and -2: common structural motif in archaeal light-driven proton pumps.	archaerhodopsin-1 and -2 (ar-1 and ar-2) are light-driven proton pumps found in halorubrum sp. aus-1 and -2, which share 55-58% sequence identity with bacteriorhodopsin (br), a proton pump found in halobacterium salinarum. in this study, ar-1 and ar-2 were crystallized into 3d crystals belonging to p4(3)2(1)2 (a = b = 128.1 a, c = 117.6 a) and c222(1) (a = 122.9 a, b = 139.5 a, c = 108.1 a), respectively. in both the crystals, the asymmetric unit contains two protein molecules with slightly diff ...	2006	16540121
[diversity of halophilic archaea in hypersaline lakes of inner mongolia, china].	the aims of this work were to explore the diversity of halophilic archaea in hypersaline lakes of inner mongolia, china and to collect novel halophilic archaea. one hundred and sixty-five halophilic archaea were isolated from the three different types of hypersaline lakes (erliannor, shangmatala and xilin soda lake) in inner mongolia. by analysis of the restriction patterns of amplified 16s rdna (ardra) with the enzyme afa i and hae ii, respectively, the isolates were clustered into 14 genotypes ...	2006	16579455
siderophores of halophilic archaea and their chemical characterization.	nine halophilic archaea viz., halobacterium salinarum, halobacterium sp.1, halobacterium sp.2, halobaculum sp., halococcus saccharolyticus, halorubrum saccharovorum, haloterrigena turkmenica, halogeometricum sp. and natrialba sp. isolated from marine salterns around bhavnagar coast were screened for siderophore production. five isolates viz., halococcus saccharolyticus, halorubrum saccharovorum, haloterrigena turkmenica, halogeometricum sp. and natrialba sp. produced siderophores as evidenced by ...	2006	16629380
[biodiversity of halophilic archaea isolated from two salt lakes in xin-jiang region of china].	there are more than 1000 salt lakes situated in northern and western regions of china and 790 of these salt lakes are in xinjiang uigur autonomous region and qinghai, tibet, inner mongolia. to better understand halophilic archaeal diversity of salt lakes in xinjiang, water and sediment samples were collected from two salt lakes, namely aibi salt lake and aiding salt lake, and the halophilic archaeal diversity of these samples was determined. totally eighty-six halophilic archeal strains, of whic ...	2006	16736571
phylogenetic relationships within the order halobacteriales inferred from 16s rrna gene sequences.	phylogenetic relationships within the halophilic archaea were inferred from comparisons of the 16s rrna gene sequences from 61 strains, representing 18 genera with validly published names within the order halobacteriales. trees produced using distance-matrix (least-squares and neighbour-joining) methods affirm with strong bootstrap support that the members of the order halobacteriales are a monophyletic group. ten genera were supported as monophyletic groups [haloarcula, halobiforma, halococcus, ...	2006	16738095
halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from ezzemoul sabkha, algeria.	a novel extremely halophilic archaeon was isolated from ezzemoul sabkha, algeria. the strain, designated 5.1(t), was neutrophilic, motile and gram-negative. at least 15 % (w/v) nacl was required for growth. the isolate grew at ph 6.5-9.0, with optimum growth at ph 7.0-7.5. mg(2+) was required for growth. polar lipids were c(20)c(20) derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate and sulfated diglycosyl diether. the genomic dn ...	2006	16825633
halorubrum lipolyticum sp. nov. and halorubrum aidingense sp. nov., isolated from two salt lakes in xin-jiang, china.	two extremely halophilic archaea, strains 9-3(t) and 31-hong(t), were isolated from aibi salt lake and aiding salt lake in xin-jiang, china. their morphology, physiology, biochemical features, polar lipid compositions and 16s rrna gene sequences were characterized in order to elucidate their taxonomic status. the results from this study indicated that strains 9-3(t) and 31-hong(t) are members of the genus halorubrum. their physiological properties and polar lipid compositions are clearly differe ...	2006	16825640
functions of carotenoids in xanthorhodopsin and archaerhodopsin, from action spectra of photoinhibition of cell respiration.	the recent discovery of a carotenoid light-harvesting antenna in xanthorhodopsin, a retinal-based proton pump in salinibacter ruber, made use of photoinhibition of respiration in whole cells to obtain action spectra [balashov et al. science 309, (2005) 2061-2064]. here we provide further details of this phenomenon, and compare action spectra in three different systems where carotenoids have different functions or efficiencies of light-harvesting. the kinetics of light-induced inhibition of respi ...	2006	17020745
halorubrum orientale sp. nov., a halophilic archaeon isolated from lake ejinor, inner mongolia, china.	a motile, pleomorphic, red-pigmented archaeon, strain ej-52t, was isolated from water from lake ejinor, a saline lake in inner mongolia, china. analysis of the almost-complete 16s rrna gene sequence showed that the isolate was phylogenetically related to species of the genus halorubrum, being most closely related to halorubrum saccharovorum atcc 29252t (96.1% sequence similarity), halorubrum lacusprofundi jcm 8891t (95.9%), halorubrum tibetense as 1.3239t (95.2%), halorubrum alcaliphilum as 1.35 ...	2006	17082390
genetic cloning and functional expression in escherichia coli of an archaerhodopsin gene from halorubrum xinjiangense.	pairs of pcr primers that targeted the archae/bacteriorhodopsin gene were used to clone the archaerhodopsin (ar) gene of halorubrum xinjiangense strain bd-1(t), and this gene was sequenced and functionally expressed in escherichia coli. recombinant e. coli cells harboring the plasmid carrying this gene became slightly purple or blue depending on whether they were supplemented with all- trans retinal or 3,4-dihydroretinal, respectively, during induction with iptg. the purple and blue membranes fr ...	2006	16075162
halorubrum alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in xinjiang, china.	a novel haloalkaliphilic archaeon, strain dz-1t, was isolated from a soda lake in xinjiang, china. the taxonomy of strain dz-1t was studied by polyphasic methods. according to 16s rrna gene sequence similarity, strain dz-1t was phylogenetically related to halorubrum tibetense (97.5 %), halorubrum vacuolatum (95.7 %) and halorubrum saccharovorum (95.9 %). strain dz-1t was able to grow at 20-44 degrees c and was also physiologically different from the above-mentioned species with respect to assimi ...	2005	15653868
growth kinetics of extremely halophilic archaea (family halobacteriaceae) as revealed by arrhenius plots.	members of the family halobacteriaceae in the domain archaea are obligate extreme halophiles. they occupy a variety of hypersaline environments, and their cellular biochemistry functions in a nearly saturated salty milieu. despite extensive study, a detailed analysis of their growth kinetics is missing. to remedy this, arrhenius plots for 14 type species of the family were generated. these organisms had maximum growth temperatures ranging from 49 to 58 degrees c. nine of the organisms exhibited ...	2005	15659670
unsaturated diether lipids in the psychrotrophic archaeon halorubrum lacusprofundi.	the major phospholipids of halorubrum lacusprofundi grown at 25 degrees c were archaeol phosphatidylglycerol, archaeol phosphatidylglycerylsulphate and archaeol phosphatidylglycerylphosphate methyl ester. glycolipids included a monoglycosyl archaeol and the sulphate ester of a diglycosyl archaeol. cultures grown at 12 degrees c contained the same suite of phospho- and glycolipids, with the addition of a series of unsaturated analogues with up to six double bonds. the patterns of unsaturation wer ...	2005	15709361
sh1: a novel, spherical halovirus isolated from an australian hypersaline lake.	a novel halovirus, sh1, with a spherical morphology is described. isolated from a hypersaline lake, sh1 is divalent, producing clear plaques on haloarcula hispanica and a natural halorubrum isolate. single-step growth curves gave a latent period of 5-6 h and a burst size of around 200 pfu/cell. the host can differentiate to form tight clusters of thick cell-walled forms, and these were shown to be resistant to infection. purified virions had no visible tail, were about 70 nm in diameter, and dis ...	2005	15823603
diversity of halophilic archaea in the crystallizers of an adriatic solar saltern.	haloarchaeal diversity in the crystallizers of adriatic secovlje salterns was investigated using gene fragments encoding 16s rrna and bacteriorhodopsin as molecular markers. screening of 180 clones from five gene libraries constructed for each gene targeted revealed 15 different 16s rrna and 10 different bacteriorhodopsin phylotypes, indicating higher haloarchaeal diversity than previously reported in such hypersaline environments. furthermore, results of rarefaction analysis indicated that anal ...	2005	16332346
osmotic shock stimulates de novo synthesis of two cardiolipins in an extreme halophilic archaeon.	the present report illustrates the response to osmotic stress of an extreme halophilic archaeon, halorubrum sp., isolated from the saltern ponds of margherita di savoia in southern italy. the hypotonic stress induces relevant changes in the membrane lipid composition: archaeal cardiolipin content markedly increases, whereas phosphatidylglycerol (pg) decreases. membranes isolated from this archaeon after cell disruption by osmotic shock are highly enriched in archaeal cardiolipin and reveal the p ...	2004	13130126
low-pass sequencing for microbial comparative genomics.	we studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile haloarcula marismortui; (2) the non-pigmented natrialba asiatica; (3) the psychrophile halorubrum lacusprofundi and (4) the dead sea isolate halobaculum gomorrense. approximately one thousand single pass genomic sequences per genome were obtained. the data were analyzed by comparative genomic analyses using the completed halobacterium sp. nrc-1 genome as a reference. low-pass shotgun sequ ...	2004	14718067
taxonomic study of halorubrum distributum and proposal of halorubrum terrestre sp. nov.	halorubrum distributum (basonym, halobacterium distributum) is an extremely halophilic, aerobic archaeon isolated from saline soils, which was described on the basis of phenotypic features of several strains. the designated type strain of the species (1m(t)=vkm b-1733(t)=jcm 9100(t)) was shown recently to differ from the other strains. in this study, halorubrum distributum isolates have been characterized with regard to phenotypic features, polar lipid content, comparison of 16s rrna gene sequen ...	2004	15023949
halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from lake zabuye in tibet, china.	a novel haloalkaliphilic archaeon, strain 8w8t, was isolated from lake zabuye, on the tibetan plateau, china. on the basis of 16s rrna gene sequence analysis, strain 8w8t was shown to belong to the genus halorubrum and was related to halorubrum vacuolatum (96.7% sequence similarity), halorubrum saccharovorum (96.0%), halorubrum lacusprofundi (95.4%) and halorubrum sodomense (95.3%). the phylogenetic distance from any species within the other genera of halobacteriales was lower than 90%. the majo ...	2004	15280294
combined use of cultivation-dependent and cultivation-independent methods indicates that members of most haloarchaeal groups in an australian crystallizer pond are cultivable.	haloarchaea are the dominant microbial flora in hypersaline waters with near-saturating salt levels. the haloarchaeal diversity of an australian saltern crystallizer pond was examined by use of a library of pcr-amplified 16s rrna genes and by cultivation. high viable counts (10(6) cfu/ml) were obtained on solid media. long incubation times (> or =8 weeks) appeared to be more important than the medium composition for maximizing viable counts and diversity. of 66 isolates examined, all belonged to ...	2004	15345408
halorubrum xinjiangense sp. nov., a novel halophile isolated from saline lakes in china.	a novel halophilic archaeon, strain bd-1t, was isolated from xiao-er-kule lake in xinjiang, china. the taxonomy of strain bd-1t was studied by polyphasic methods. according to 16s rrna gene sequence similarity, strain bd-1t was phylogenetically related to halorubrum trapanicum (98.4 %), halorubrum sodomense (98.0 %), halorubrum distributum (97.8 %) and halorubrum coriense (97.3 %). strain bd-1t is able to grow at 10 degrees c and further differs physiologically from the above species in the assi ...	2004	15388744
frequent recombination in a saltern population of halorubrum.	sex and recombination are driving forces in the evolution of eukaryotes. homologous recombination is known to be the dominant process in the divergence of many bacterial species. for archaea, the only direct evidence bearing on the importance or natural occurrence of homologous recombination is anecdotal reports of mosaicism from comparative genomic studies. genetic studies, however, reveal that recombination may play a significant role in generating diversity among members of at least one archa ...	2004	15591201
formation of insoluble magnesium phosphates during growth of the archaea halorubrum distributum and halobacterium salinarium and the bacterium brevibacterium antiquum.	stationary phase cells of the halophilic archaea halobacterium salinarium and halorubrum distributum, growing at 3-4 m nacl, and of the halotolerant bacterium brevibacterium antiquum, growing with and without 2.6 nacl, took up approximately 90% of the phosphate from the culture media containing 2.3 and 11.5 mm phosphate. the uptake was blocked by the uncoupler fccp. in b. antiquum, edta inhibited the phosphate uptake. the content of polyphosphates in the cells was significantly lower than the co ...	2004	16329899
[archaeal diversity of zabuye lake in tibet analyzed by culture-independent approach].	with culture-independent approach, microbial dna was directly extracted from samples of zabuye saline soda lake. using the microbial dna as template, archaeal 16s rdnas were amplified by pcr. amplified products were cloned and sequenced. 60 different cloned partial sequences, most of which were related to haloalkaliphilic archaeon, were acquired. in the phylogenetic tree, some clones of zabuye lake belonged to genus natronobacterium, natrinema, natronococcus, natronorubrum, natronomonas, halorub ...	2003	16276911
strain ncimb 13488 may serve as the type strain of halorubrum trapanicum. opinion 74.	the judicial commission of the international committee on systematics of prokaryotes decided that strain ncimb 13488 may serve as the type strain of halorubrum trapanicum.	2003	12807224
purification and biological characterization of halocin c8, a novel peptide antibiotic from halobacterium strain as7092.	halocins are bacteriocin-like proteins or peptides produced by many species of the family halobacteriaceae. halocin c8, excreted by the halobacterium strain as7092, is a single 6.3-kda polypeptide with an isoelectric point of 4.4, which is sensitive to proteinase k but not to trypsin. halocin c8 is quite stable, as it can be desalted, boiled, frozen, subjected to organic solvents, and stored in culture supernatant at 4 degrees c or in dh(2)o at -20 degrees c for more than 1 year without losing a ...	2003	12811620
organic solvent tolerance of halophilic archaea.	organic solvent tolerance was tested in type strains of type species of the sixteen genera of halobacteriaceae, the halophilic archaea. most of the strains were observed to grow in the presence of hexylether (log pow=5.1), but none grew in the presence of n-octane (log pow=4.9) except halogeometricum borinquense jcm 10706t and halorubrum saccharovorum jcm 8865t. on the other hand, two strains, haloarcula spp. ohf-1 and 2 isolated from a french solar salt were found to show stronger tolerance eve ...	2003	12951519
halorubrum tebenquichense sp. nov., a novel halophilic archaeon isolated from the atacama saltern, chile.	a novel extremely halophilic archaeon was isolated from lake tebenquiche, situated in the northern part of the atacama saltern, chile. the cells of these micro-organisms were mostly irregularly disc-shaped. they grew in medium containing saturated concentrations of nacl and did not require magnesium for optimal growth. the polar lipid composition revealed the presence of mannosyl-2-sulfate-(1-4)-glycosyl-archaeol, the main glycolipid of the genus halorubrum, and two new glycolipids. the g+c cont ...	2002	11837297
hf2: a double-stranded dna tailed haloarchaeal virus with a mosaic genome.	hf2 is a haloarchaeal virus infecting two halorubrum species (family halobacteriaceae). it is lytic, has a head-and-tail morphology and belongs to the myoviridae (contractile tails). the linear double-stranded dna genome was sequenced and found to be 77 670 bp in length, with a mol% g+c of 55.8. a total of 121 likely open reading frames (orfs) were identified, of which 37 overlapped at start and stop codons. the predicted proteins were usually acidic (average pi of 4.8), and less than about 12% ...	2002	11967086
pcr and blot hybridization for rapid identification of haloferax species.	based on the amplification of a 16s rdna, a pcr assay for the identification of species of haloferax to genus level was performed. two variable regions of the 16s rdna in haloferax spp. were selected as genus-specific primers for the pcr assay and hybridization probe. five genera of halophilic archaea and escherichia coli were examined as outside groups. using this approach, all strains of haloferax spp. were positive. in contrast, all species belonging to the most closely related genera, includ ...	2002	12109888
diversity of archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies.	the diversity of archaea from three different hypersaline environments was analyzed and compared by polymerase chain reaction (pcr)-based molecular phylogenetic techniques and cultivation approaches. the samples originated from a crystallization pond of a solar saltern in spain (fc); an alkaline lake in nevada, usa, (emf); and a small pond from a slag heap of a potassium mine in germany (die). except for two 16s rdna sequences that were related to crenarchaeota from soil and did not apparently b ...	2002	12215811
archaeal biodiversity in crystallizer ponds from a solar saltern: culture versus pcr.	the culturable haloarchaeal diversity in a crystallizer pond from a solar saltern has been analyzed and compared with the biodiversity directly retrieved by analysis of rrna genes amplified from the environment. two different sets of culture conditions have been assayed: solid medium with yeast extract as carbon source and liquid media with either yeast extract or a mixture of fishmeal, spirulina sp., and artemia salina. seventeen colonies grown on plates with yeast extract incubated at 30 degre ...	2001	11252160
mechanisms of acetate formation and acetate activation in halophilic archaea.	the halophilic archaea halococcus (hc.) saccharolyticus, haloferax (hf.) volcanii, and halorubrum (hr.) saccharovorum were found to generate acetate during growth on glucose and to utilize acetate as a growth substrate. the mechanisms of acetate formation from acetyl-coa and of acetate activation to acetyl-coa were studied. hc. saccharolyticus, exponentially growing on complex medium with glucose, formed acetate and contained adp-forming acetyl-coa synthetase (adp-acs) rather than acetate kinase ...	2001	11409546
lipid membranes from halophilic and alkali-halophilic archaea have a low h+ and na+ permeability at high salt concentration.	the influence of ph and the salt concentration on the proton and sodium ion permeability of liposomes formed from lipids of the halophile halobacterium salinarum and the haloalkaliphile halorubrum vacuolatum were studied. in contrast with liposomes formed from escherichia coli lipids, liposomes formed from halophilic lipids remained stable up to 4m of nacl and kcl. the proton permeability of the liposomes from lipids of halophiles was independent of the salt concentration and was essentially con ...	1999	10591015
diversity of extremely halophilic bacteria.	in this review, the history of the classification of the family halobacteriaceae, the extremely halophilic aerobic archaea, is reviewed with some emphasis on the recently described new genera halobaculum, halorubrum, natrialba, natronomonas, and "haloterrigena." speculation is made about the evolutionary relationship between members of the halobacteriaceae and the extremely halophilic, anaerobic methanogens of the genera methanohalobium and methanohalophilus. efforts to find missing links betwee ...	1998	9783176
diversity of alkaliphilic halobacteria: proposals for transfer of natronobacterium vacuolatum, natronobacterium magadii, and natronobacterium pharaonis to halorubrum, natrialba, and natronomonas gen. nov., respectively, as halorubrum vacuolatum comb. nov., natrialba magadii comb. nov., and natronomonas pharaonis comb. nov., respectively.	the 16s rrna genes of three species of the genus natronobacterium (natronobacterium gregoryi, natronobacterium pharaonis, and natronobacterium vacuolatum) were sequenced and compared to that of the previously sequenced species natronobacterium magadii. the sequences revealed that natronobacterium pharaonis was phylogenetically distinct from the other members of the genus and also from other recognized genera of the family halobacteriaceae. however, natronobacterium vacuolatum and natronobacteriu ...	1997	9226918