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PubMed1998

Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico.

A novel extremely halophilic archaeon was isolated from the solar salterns of Cabo Rojo, Puerto Rico. The organism is very pleomorphic, motile and requires at least 8% (w/v) NaCl to grow. Polar lipid composition revealed the presence of a novel non-sulfate-containing glycolipid and the absence of the glycerol diether analogue of phosphatidylglycerosulfate. The G + C content of the DNA is 59 mol%. On the basis of 16S rRNA sequence data, the new isolate cannot be classified in one of the recognized genera, but occupies a position that is distantly related to the genus Haloferax. All these features justify the creation of a new genus and a new species for the family Halobacteriaceae, order Halobacteriales. The name Halogeometricum borinquense gen. nov., sp. nov. is proposed. The type strain is ATCC 700274T.

Base Composition↗

PubMed2000

Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah.

Strain AX-2T (T = type strain) was isolated from sediment of Great Salt Lake, Utah, USA. Optimal salinity for growth was 27% (w/v) NaCl and only a few carbohydrates supported growth of the strain. Strain AX-2T did not grow on complex substrates such as yeast extract or peptone. 16S rRNA analysis revealed that strain AX-2T was a member of the phyletic group defined by the family Halobacteriaceae, but there was a low degree of similarity to other members of this family. The polar lipid composition comprising phosphatidyl glycerol, the methylated derivative of diphosphatidyl glycerol, triglycosyl diethers and sulfated triglycosyl diethers, but not phosphatidyl glycerosulfate, was not identical to that of any other aerobic, halophilic species. On the basis of the data presented, it is proposed that strain AX-2T should be placed in a new taxon, for which the name Halorhabdus utahensis is appropriate. The type strain is strain AX-2T (= DSM 12940T).

Base Composition↗

PubMed2002

Halomicrobium mukohataei gen. nov., comb. nov., and emended description of Halomicrobium mukohataei.

Haloarcula mukohataei, previously isolated from soils of salt flats in Argentina, was originally placed in the genus Haloarcula on the basis of 16S rRNA gene sequence comparison. However, its morphology and polar lipid composition differs from that of the other Haloarcula species. In addition, its phylogenetic distance from other Haloarcula species is rather large, and the 16S rDNA sequence does not contain many of the signature bases characteristic of the genus. Transfer of the species to a new genus was therefore recommended by the International Committee on Systematic Bacteriology Subcommittee on the taxonomy of Halobacteriaceae. A full description of the isolate, proposed as a member of a new genus, Halomicrobium, as Halomicrobium mukohataei comb. nov., is presented. The type strain is strain arg-2T (= JCM 9738T = DSM 12286T = ATCC 700874T = NCIMB 13541T).

DNA, Archaeal↗

PubMed2002

Characterization of a novel halophilic archaeon, Halobiforma haloterrestris gen. nov., sp. nov., and transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov.

Strain 135(T), a novel red-pigmented, aerobic, extremely halophilic member of the Archaea showing rod, coccus and slightly pleomorphic morphology, was isolated from hypersaline soil close to Aswan (Egypt). This organism is neutrophilic, motile and requires at least 2.2 M NaCl, but no MgCl2, for growth and exhibits optimal growth at 42 degrees C. Polar lipid analysis revealed the presence of sulfated triglycosyl diether and triglycosyl diether as the sole glycolipids as well as the absence of the glycerol diether analogue of phosphatidyl glycerosulfate. C20:C20 and C20:C25 core lipids are present in almost equal proportions. The G+C content of the DNA is 66.9 mol%. 16S rDNA analysis revealed that strain 135(T) was a member of the phyletic group defined by the family Halobacteriaceae, but there was a low degree of similarity to other members of this family. Highest similarity values of 96.4 and 93.8-94.3% were obtained to the 16S rDNA of Natronobacterium nitratireducens and Natronobacterium gregoryi, Natronococcus occultus and Natronococcus amylolyticus. Strain 135(T) is able to accumulate polyhydroxybutyrate as intracellular reserve material. On the basis of the data presented, strain 135(T) should be placed in a new genus, Halobiforma gen. nov. as Halobiforma haloterrestris sp. nov. The type strain is strain 135(T) (= DSM 13078(T) = JCM 11627(T)). Moreover, the transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov. is proposed.

Base Composition↗

PubMed2006

Halovivax asiaticus gen. nov., sp. nov., a novel extremely halophilic archaeon isolated from Inner Mongolia, China.

Strain EJ-46T, a novel pleomorphic, aerobic, extremely halophilic member of the Archaea was isolated from sediment of the saline Lake Ejinor, in Inner Mongolia, China. This organism was neutrophilic and required at least 15 % (2.5 M) NaCl for growth. MgCl2 was not required. The isolate was able to grow at pH 6.0-9.0. Optimum growth occurred in media containing 20 % (3.4 M) NaCl at pH 7.0-7.5. Polar lipid analysis revealed the presence of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, derived from both C20C20 and C20C25 glycerol diethers. Four glycolipids were detected, one of which may be novel. The DNA G+C content was 60.3 mol%. 16S rRNA gene analysis revealed that strain EJ-46T was a member of the phylogenetic group defined by the family Halobacteriaceae, and the highest 16S rRNA gene similarity values of 94.9 and 94.8 % were obtained with the haloalkaliphilic species of the genus Natronococcus, Natronococcus occultus and Natronococcus amylolyticus, respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the novel isolate should be classified as representing a new genus and species, for which the name Halovivax asiaticus gen. nov., sp. nov. is proposed. The type strain is EJ-46T (=CGMCC 1.4248T = CECT 7098T).

China↗

PubMed2006

Natrinema ejinorense sp. nov., isolated from a saline lake in Inner Mongolia, China.

A Gram-negative, non-motile, neutrophilic, pleomorphic and extremely halophilic archaeon, strain EJ-57T, was isolated from saline Lake Ejinor in Inner Mongolia, China. Strain EJ-57T was able to grow at 25-50 degrees C, required at least 1.8 M NaCl for growth (optimum at 3.4 M NaCl) and grew over a pH range from 6.0 to 8.5 (optimum at pH 7.0). Hypotonic treatment with less than 1.5 M NaCl caused cell lysis. Analysis of the almost complete 16S rRNA gene sequence indicated that the isolate represented a member of the genus Natrinema in the family Halobacteriaceae. Strain EJ-57T was most closely related to Natrinema versiforme JCM 10478T (96.2% sequence similarity), Natrinema pallidum NCIMB 777T (95.9% sequence similarity), Natrinema altunense JCM 12890T (95.8% sequence similarity) and Natrinema pellirubrum NCIMB 786T (95.5 % sequence similarity). However, DNA-DNA hybridization experiments showed that strain EJ-57T was not related to these species, with levels of DNA-DNA relatedness equal to or below 39%. The major polar lipids of the isolate were C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and the disulfated glycolipid S2-DGA-1. The G+C content of the genomic DNA was 64.7 mol%. Comparative analysis of phenotypic characteristics between strain EJ-57T and recognized Natrinema species supported the conclusion that EJ-57T represents a novel species within this genus, for which the name Natrinema ejinorense sp. nov. is proposed. The type strain is EJ-57T (=CECT 7144T=JCM 13890T=CGMCC 1.6202T).

Base Composition↗

PubMed2007

Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, sulfide-rich spring.

Two novel strains of halophilic archaea, DX253(T) and GY252, were isolated from Zodletone Spring, a low-salt, sulfide- and sulfur-rich spring in south-western Oklahoma, USA. The cells were cocci or coccobacilli and occurred singly or in pairs. The two strains grew in a wide range of salt concentrations (0.8-5.1 M) and required at least 5 mM Mg(2+) for growth. The pH range for growth was 5-7.5 and the temperature range was 25-45 degrees C. In addition to having the capacity to grow at relatively low salt concentrations, cells remained viable in distilled water after prolonged incubation. The two diether phospholipids that are typical of members of the order Halobacteriales, phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, were present. Phosphatidylglycerol sulfate and two unidentified glycolipids were also detected. Each strain had two distinct 16S rRNA gene sequences that were only 89.5-90.8 % similar to sequences from the most closely related cultured and recognized species within the order Halobacteriales. The DNA G+C content of the type strain was found to be 60.5 mol%. The closest relatives were clones and uncharacterized isolates obtained from coastal salt-marsh sediments with salinities equivalent to that of seawater. The physiological, biochemical and phylogenetic differences between strains DX253(T) and GY252 and other previously described genera of extremely halophilic archaea suggest that these novel strains represent a novel species and genus within the family Halobacteriaceae, for which the name Haladaptatus paucihalophilus gen. nov., sp. nov. is proposed. The type strain is DX253(T) (=JCM 13897(T)=DSM 18195(T)=ATCC BAA-1313(T)=KCTC 4006(T)).

DNA, Archaeal↗

PubMed1998

Typing of halophilic Archaea and characterization of their cell surface carbohydrates by use of lectins.

Lectins are important tools for cell typing and for the study of cell surface components. They have been widely used for the analysis of carbohydrates on the surface of many eukaryotic and prokaryotic cells, but they have not yet been exploited in the study of the halophilic Archaea (family Halobacteriaceae), because of the high salinity required for the structural integrity of these microorganisms. We have defined the salt concentration threshold high enough for survival of the Archaea, but sufficiently low for lectins to bind to them. Under these conditions we studied the interactions of a series of lectins, exhibiting different sugar specificities, with diverse halophilic Archaea. Concanavalin A was the most reactive by virtue of its glucose (and mannose) binding. The other lectins varied in their interactions. The results indicate that lectins might be useful probes for both archaeal typing and analysis of their cell surface carbohydrates.

Bacterial Typing Techniques↗

PubMed2004

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 the family Halobacteriaceae, including members related to species of the genera Haloferax, Halorubrum, and Natronomonas. In addition, isolates belonging to a novel group (the ADL group), previously detected only as 16S rRNA genes in an Antarctic hypersaline lake (Deep Lake), were cultivated for the first time. The 16S rRNA gene library identified the following five main groups: Halorubrum groups 1 and 2 (49%), the SHOW (square haloarchaea of Walsby) group (33%), the ADL group (16%), and the Natronomonas group (2%). There were two significant differences between the organisms detected in cultivation and 16S rRNA sequence results. Firstly, Haloferax spp. were frequently isolated on plates (15% of all isolates) but were not detected in the 16S rRNA sequences. Control experiments indicated that a bias against Haloferax sequences in the generation of the 16S rRNA gene library was unlikely, suggesting that Haloferax spp. readily form colonies, even though they were not a dominant group. Secondly, while the 16S rRNA gene library identified the SHOW group as a major component of the microbial community, no isolates of this group were obtained. This inability to culture members of the SHOW group remains an outstanding problem in studying the ecology of hypersaline environments.

Archaea↗

PubMed1995

Diversity of lactate metabolism in halophilic archaea.

D-Lactate is readily used as a substrate for the growth of species of halophilic archaea belonging to the genera Haloferax and Haloarcula. L-Lactate was used by Haloferax species (Haloferax volcanii, Haloferax mediterranei) only when a substantial concentration of the D-isomer was also present in the medium. On the enzymatic level, considerable diversity was found in the lactate metabolism of the different representatives of the Halobacteriaceae. At least three types of lactate dehydrogenases were detected in halophilic archaea. A high level of activity of an NAD-linked enzyme was present constitutively in Haloarcula species, and a low level of activity was also detected in Haloferax mediterranei. NAD-independent lactate dehydrogenases, oxidizing L-lactate and D-lactate with 2,6-dichlorophenol-indophenol as electron acceptor, were detected in all nine species tested, but L-lactate dehydrogenase activity in Halobacterium species was very low, and Haloarcula species, which possess a high level of activity of NAD-linked lactate dehydrogenase, showed very low activities of both NAD-independent D- and L-lactate dehydrogenase. An inducible lactate racemase, displaying an unusually high pH optimum, was found in Haloferax volcanii. Lactate racemase activity was found constitutively in Haloarcula species, but no activity was detected in Halobacterium species and in Haloferax mediterranei.

Halobacteriaceae↗

PubMed2004

Phylogenetic analysis of bacterial populations in waters of the former Texcoco Lake, Mexico.

Molecular techniques were used to compare the compositions of the bacterial communities of the 2 following lagoons from the former soda Texcoco Lake, Mexico: the restored Facultativa lagoon and the Nabor Carrillo lagoon. Ribosomal intergenic spacer analysis (RISA) revealed that bacterial communities of the 2 lagoons were different and presented a relatively low diversity. Clone libraries of 16S rDNA genes were constructed, and significant phylotypes were distinguished by restriction fragment length polymorphism (RFLP). A representative clone from each phylotype was partially sequenced. Molecular identification and phylogenetic analyses based on ribosomal sequences revealed that the Facultativa lagoon harbored mainly gamma- and beta-Proteobacteria, low G+C Gram-positive bacteria, and several members of the Halobacteriaceae family of archaea. The Nabor Carrillo lagoon mainly included typical halophilic and alkaliphilic low G+C Gram-positive bacteria, gamma-Proteobacteria, and beta-Proteobacteria similar to those found in other soda lakes. Several probably noncultured new bacterial species were detected. Three strains were isolated from the Nabor Carrillo lagoon, their partial 16S rDNA sequences were obtained. On this basis, they were identified as Halomonas magadiensis (H1), Halomonas eurihalina (H2), and Staphylococcus sciuri (H3). This is the first study that uses molecular techniques to investigate potential genetic diversity in the Texcoco lakes. In this preliminary evaluation, we infer the presence of alkalophilic, halophilic, or haloalkaliphilic bacteria potentially useful for biotechnology.

Archaea↗

PubMed2003

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 even to isooctane (log Pow=4.8). Growth of some strains was retarded by the presence of n-decane but reached to the same cell densities at late stationary phase. Final cell densities of some strains were greatly repressed by the presence of the solvent.

Alkanes↗

PubMed1994

Enzyme diversity in halophilic archaea.

The halophilic archaea display a considerable extent of enzyme diversity. The presence or absence of certain enzymatic activities is closely linked with the taxonomic status of the strains investigated. Thus, Halobacterium species such as Hb. salinarium, Hb. halobium, and Hb. cutirubrum differ from most other Halobacteriaceae tested by the possession of an NAD(+)-dependent glycerol dehydrogenase, by the absence of methylglyoxal synthase activity, and the ability of fermentative growth on arginine. Species such as Hb. saccharovorum and Hb. sodomense, which are still classified within the genus Halobacterium, have an enzymatic machinery greatly different from that of the Hb. salinarium-Hb. halobium group, confirming the need for a taxonomic reappraisal of these species. The presence of NAD(+)-dependent D-lactate dehydrogenase is characteristic of representatives of the genus Haloarcula, which possess only low activities of NAD(+)-independent L- and D-lactate dehydrogenases, if at all. Other enzymes which show considerable diversity are fructose 1,6-bisphosphate aldolase, of which two classes exist, and ribulose 1,6-bisphosphate carboxylase, which is present in a limited number of species.

Bacterial Proteins↗

PubMed1998

An overview of the role and diversity of compatible solutes in Bacteria and Archaea.

The accumulation of compatible solutes is a prerequisite for the adaptation of microorganisms to osmotic stress imposed by salt or organic solutes. Two types of strategies exist to cope with high external solute concentrations; one strategy is found in the extremely halophilic Archaea of the family Halobacteriaceae and the Bacteria of the order Haloanaerobiales involving the accumulation of inorganic ions. The other strategy of osmoadaptation involves the accumulation of specific organic solutes and is found in the vast majority of microorganisms. The organic osmolytes range from sugars, polyols, amino acids and their respective derivatives, ectoines and betaines. The diversity of these organic solutes has increased in the past few years as more organisms, especially thermophilic and hyperthermophilic Bacteria and Archaea, have been examined. The term compatible solute can also be applied to solutes that protect macromolecules and cells against stresses such as high temperature, desiccation and freezing. The mechanisms by which compatible solutes protect enzymes, cell components and cells are still a long way from being thoroughly elucidated, but there is a growing interest in the utilization of these solutes to protect macromolecules and cells from heating, freezing and desiccation.

Archaea↗

PubMed2002

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 belong to the indigenous halophilic community, all sequences recovered from environmental DNA or cultivated strains grouped within the Halobacteriaceae. Mostly 16S rDNA sequences related to the genera Halorubrum and Haloarcula were detected in sample FC, and organisms belonging to these genera were also recovered by cultivation. In contrast, sequences related to five different groups of halophilic archaea were amplified from sample DIE (including novel lineages with only uncultivated phylotypes), but the organisms that were cultivated from this sample fell into different groups (i.e., Natronococcus, Halorubrum, or unaffiliated) and did not overlap with those predicted using the culture-independent approach. With respect to the highly alkaline sample, EMF, four groups were predicted from the environmental 16S rDNA sequences, two of which ( Natronomonas and Haloarcula) were also recovered through cultivation together with Natronococcus isolates. In summary, we found that halophilic archaea dominate the archaeal populations in these three hypersaline environments and show that culturability of the organisms predicted by molecular surveys might strongly depend on the habitat chosen. While a number of novel halophilic archaea have been isolated, we have not been able to cultivate representatives of the new lineages that were detected in this and several other environmental studies.

Archaea↗

PubMed2003

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 activity. The purification of this halocin was achieved by combination of tangential flow filtration (TFF), Sephadex G50 and DEAE-sepharose chromatography. The N-terminal amino acid sequence was also determined by Edman degradation. Halocin C8 appeared to have a very wide activity spectrum, including most haloarchaea and even some haloalkaliphilic rods. When a sensitive strain of Halorubrum saccharovorum was exposed to halocin C8, the treated cells swelled at the initial stage, the cell wall appeared to be nicked and the cytoplasm was then extruded out, and the whole cell was eventually completely lysed. These results indicate that halocin C8 is a novel microhalocin and its primary target might be located in the cell wall of the sensitive cells.

Amino Acid Sequence↗

PubMed2004

Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China.

Three novel isolates of haloalkaliphilic archaea, strains IHC-005T, IHC-010, and N-1311T, from soda lakes in Inner Mongolia, China, were characterized to elucidate their taxonomic positions. The three strains were aerobic, Gram-negative chemoorganotrophs growing optimally at 37-45 degrees C, pH 9.0-9.5, and 15-20% NaCl. Cells of strains IHC-005T/IHC-010 were motile rods, while those of strain N-1311T were non-motile pleomorphic flats or cocci. The three strains contained diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester. No glycolipids were detected. On phylogenetic analysis of 16S rRNA gene sequences, they formed an independent cluster in the Natro group of the family Halobacteriaceae. Comparison of their morphological, physiological, and biochemical properties, DNA G + C content and 16S rRNA gene sequences, and DNA-DNA hybridization study support the view that strains IHC-005T/IHC-010 and strain N-1311T represent separate species. Therefore, we propose Natronolimnobius baerhuensis gen. nov., sp. nov. for strains IHC-005T (=CGMCC 1.3597T =JCM 12253T)/IHC-010 (=CGMCC 1.3598 = JCM 12254) and Natronolimnobius innermongolicus sp. nov. for N-1311T (=CGMCC 1.2124T =JCM 12255T).

Archaea↗

PubMed2002

Amino acid composition of bulk protein and salt relationships of selected enzymes of Salinibacter ruber, an extremely halophilic bacterium.

The extremely halophilic bacterium Salinibacter ruber was previously shown to have a high intracellular potassium content, comparable to that of halophilic Archaea of the family Halobacteriaceae. The amino acid composition of its bulk protein showed a high content of acidic amino acids, a low abundance of basic amino acids, a low content of hydrophobic amino acids, and a high abundance of serine. We tested the level of four cytoplasmic enzymatic activities at different KCl and NaCl concentrations. Nicotinamide adenine dinucleotide (NAD)-dependent isocitrate dehydrogenase functioned optimally at 0.5-2 M KCl, with rates of 60% of the optimum value at 3.3 M. NaCl provided less activation: 70% of the optimum rates in KCl were found at 0.2-1.2 M NaCl, and above 3 M NaCl, activity was low. We also detected nicotinamide adenine dinucleotide phosphate (NADP)-dependent isocitrate activity, which remained approximately constant between 0-3.2 M NaCl and increased with increasing KCl concentration. NAD-dependent malate dehydrogenase functioned best in the absence of salt, but rates as high as 25% of the optimal values were measured in 3-3.5 M KCl or NaCl. NAD-dependent glutamate dehydrogenase, assayed by the reductive amination of 2-oxoglutarate, showed low activity in the absence of salt. NaCl was stimulatory with optimum activity at 3-3.5 M. However, no activity was found above 2.5 M KCl. Although the four activities examined all function at high salt concentrations, the behavior of individual enzymes toward salt varied considerably. The results presented show that Salinibacter enzymes are adapted to function in the presence of high salt concentrations.

Amino Acids↗