Salimicrobium flavidum sp. nov., isolated from a marine solar saltern

A Gram-variable-staining, motile and coccoid-, ovoid- or rod-shaped bacterium, strain ISL-25(T), was isolated from a marine solar saltern of the Yellow Sea, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain ISL-25(T) grew optimally at pH 7.0-8.0 and 30-37 degrees C. Strain ISL-25(T) contained meso-diaminopimelic acid as the cell-wall peptidoglycan, MK-7 as the predominant menaquinone and anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0) as the major fatty acids. The DNA G+C content was 49.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ISL-25(T) belongs to the genus Salimicrobium. The similarity values between the 16S rRNA gene sequence of strain ISL-25(T) and those of the type strains of the three currently recognized Salimicrobium species were 97.6-98.3 %. Mean DNA-DNA relatedness values between strain ISL-25(T) and the type strains of the genus Salimicrobium were 9-15 %. Differential phenotypic properties of strain ISL-25(T), together with the phylogenetic and genetic distinctiveness, revealed that this strain could be differentiated from other Salimicrobium species. Therefore, strain ISL-25(T) represents a novel species within the genus Salimicrobium, for which the name Salimicrobium flavidum sp. nov. is proposed. The type strain is ISL-25(T) (=KCTC 13260(T)=CCUG 56755(T)).

Thalassobacillus cyri sp. nov., a moderately halophilic Gram-positive bacterium from a hypersaline lake

A Gram-positive, moderately halophilic bacterium, designated strain HS286(T), was isolated from water of the hypersaline Lake Howz-Soltan in Iran. Cells were strictly aerobic, rod-shaped, motile and able to produce ellipsoidal endospores at a central-subterminal position in swollen sporangia. Isolate HS286(T) grew in a complex medium supplemented with 1-15 % (w/v) NaCl, with optimum growth at 8.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain HS286(T) was closely related to Thalassobacillus devorans G-19.1(T) (99.4 % gene sequence similarity). The other closest species were Halobacillus yeomjeoni MSS-402(T) (96.9 %) and other species of the genus Halobacillus (with 96.7-93.5 % similarity). Strain HS286(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the respiratory isoprenoid quinone. The major fatty acids were anteiso-C(15 : 0) (43.8 %), iso-C(16 : 0) (21.4 %), iso-C(14 : 0) (9.4 %), anteiso-C(17 : 0) (8.7 %) and iso-C(15 : 0) (7.0 %) and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, two phospholipids and a glycolipid. The DNA G+C content was 43.0 mol%. All of these features confirmed the placement of isolate HS286(T) within the genus Thalassobacillus. However DNA-DNA hybridization between strain HS286(T) and the only recognized species of the genus Thalassobacillus, T. devorans G-19.1(T), was 27.3 %, showing unequivocally that the novel isolate constituted a new genospecies. Strain HS286(T) could be clearly differentiated from T. devorans and other phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain HS286(T) constitutes a novel species, for which the name Thalassobacillus cyri sp. nov. is proposed. The type strain is HS286(T) (=CCM 7597(T)=JCM 15722(T)).

[Characterization of a thermophilic Geobacillus strain DM-2 degrading hydrocarbons]

A thermophilic Geobacillus strain DM-2 from a deep-subsurface oil reservoir was investigated on its capability of degrading crude oil under various conditions as well as its characters on degrading hydrocarbons in optimal conditions. The results showed that Geobacillus strain DM-2 was able to degrade crude oil under anoxic wide-range conditions with pH ranging from 4.0 to 10.0, high temperature in the range of 45-70 degrees C and saline concentration ranging from 0.2% to 3.0%. Furthermore, the optimal temperature and pH value for utilizing hydrocarbons by the strain were 60 degrees C and 7.0, respectively. Under such optimal conditions, the strain utilized liquid paraffine emulsified by itself as its carbon source for growth; further analysis by gas chromatography (GC) and infrared absorption spectroscopy demonstrated that it was able to degrade n-alkanes (C14-C30), branched-chain alkanes and aromatic hydrocarbons in crude oil and could also utilize long-chain n-alkanes from C16 to C36, among of which the degradation efficiency of C28 was the highest, up to 88.95%. One metabolite of the strain oxidizing alkanes is fatty acid.While utilizing C16 as carbon source for 5 d, only one fatty acid-acetic acid was detected by HPLC and MS as the product, with the amount of 0.312 g/L, which indicated that it degraded n-alkanes with pathway of inferior terminal oxidation,and then followed by a beta-oxidation pathway. Due to its characters of efficient emulsification, high-performance degradation of hydrocarbons and fatty-acid production under high temperature and anoxic condition, the strain DM-2 may be potentially applied to oil-waste treatment and microbial enhanced heavy oil recovery in extreme conditions.

Microbial Biosynthesis of Polyglutamic Acid Biopolymer and Applications in the Biopharmaceutical, Biomedical and Food Industries

This review article provides an updated critical literature review on the production and applications of Polyglutamic Acid (PGA). alpha-PGA is synthesized chemically, whereas gamma-PGA can be produced by a number of microbial species, most prominently various Bacilli. Great insight into the microbial formation of gamma-PGA has been gained thanks to the development of molecular biological techniques. Moreover, there is a great variety of applications for both isoforms of PGA, many of which have not been discovered until recently. These applications include: wastewater treatment, food products, drug delivery, medical adhesives, vaccines, PGA nanoparticles for on-site drug release in cancer chemotherapy, and tissue engineering.

Structure, function and biosynthesis of carotenoids in the moderately halophilic bacterium Halobacillus halophilus

Inhibitor studies and mutant analysis revealed a C(30) pathway via 4,4'-diapophytoene and 4,4'-diaponeurosporene to 4,4'-diaponeursoporene-4-oic acid esters related to staphyloxanthin in Halobacillus halophilus. Six genes may be involved in this biosynthetic pathway and could be found in two adjacent gene clusters. Two genes of this pathway could be functionally assigned by functional pathway complementation as a 4,4'-diapophytoene synthase and a 4,4'-diapophytoene desaturase gene. These genes were organized in two operons together with two putative oxidase genes, a glycosylase and an acyl transferase ortholog. Pigment mutants were obtained by chemical mutagenesis. Carotenoid analysis showed that a white mutant accumulated 4,4'-diapophytoene due to a block in desaturation. In a yellow mutant carotenogenesis was blocked at the stage of 4,4'-diaponeurosporene and in an orange mutant at the stage of 4,4'-diaponeurosporene-4-oic acid. The protective function of these pigments could be demonstrated for H. halophilus after inhibition of carotenoid synthesis by initiation of oxidative stress. A degree of oxidative stress which still allowed 50% growth of carotenogenic cells resulted in the death of the cells devoid of colored carotenoids.

[The high ethanol tolerance in a thermophilic bacterium Anoxybacillus sp. WP06]

Anoxybacillus sp. WP06 is a thermophilic (optimum temperature for growth, 60 degrees C), facultative anaerobe. Strain WP06 is able to utilize a wide range of carbon sources such as glucose, xylose, arabinose, starch, maltose and sorbitol. Anaerobically, glucose and xylose were fermented to ethanol as minor products. Unlike most thermophilic bacteria isolated to date, strain WP06 is tolerant (maintained viability) to high ethanol concentrations up to 15% at 60 degrees C. The growth rate was slightly inhibited at 8% ethanol. The observation that strain WP06 exhibits higher tolerance of 15% ethanol at 60 degrees C exploits the level of ethanol tolerance in thermophilic bacteria. Strain WP06 may be candidate for mechanisms of ethanol tolerance in thermophilic bacteria.

Characterization of growth-supporting factors produced by Geobacillus toebii for the commensal thermophile Symbiobacterium toebii

Symbiobacterium toebii is a commensal symbiotic thermophile that cannot grow without support from a partner bacterium. We investigated the properties of Symbiobacterium growth-supporting factors (SGSFs) produced by the partner bacterium Geobacillus toebii. SGSFs occurred in both the cell-free extract (CFE) and culture supernatant of G. toebii and might comprise multifarious materials because of their different biological properties. The heavy SGSF contained in the cytosolic component exhibited heat- and proteinase-sensitive proteinaceous properties and had a molecular mass of >50 kDa. In contrast, the light SGSF contained in the extracellular component exhibited heat-stable, proteinase-resistant, nonprotein properties and had a molecular mass of <10 kDa. Under morphological examination using light microscopy, S. toebii cultured with the culture supernatant of G. toebii was filamentous, whereas S. toebii cultured with the CFE of G. toebii was rod-shaped. These results strongly suggest that the SGSFs produced by G. toebii comprise two or more types that differ in their growth-supporting mechanisms, although all support the growth of S. toebii. Upon the examination of the distribution of SGSFs in other bacteria, both cytosolic and extracellular components of Geobacillus kaustophilus, Escherichia coli, and Bacillus subtilis had detectable growth-supporting effects for S. toebii, indicating that common SGSF materials are widely present in various bacterial strains.

Isolation and characterization of a potential paraffin-wax degrading thermophilic bacterial strain Geobacillus kaustophilus TERI NSM for application in oil wells with paraffin deposition problems

Paraffin deposition problems, that have plagued the oil industry, are currently remediated by mechanical and chemical means. However, since these methods are problematic, a microbiological approach has been considered. The bacteria, required for the mitigation of paraffin deposition problems, should be able to survive the high temperatures of oil wells and degrade the paraffins under low oxygen and nutrient conditions while sparing the low carbon chain paraffins. In this study, a thermophilic paraffinic wax degrading bacterial strain was isolated from a soil sample contaminated with paraffinic crude oil. The selected strain, Geobacillus TERI NSM, could degrade 600mg of paraffinic wax as the sole carbon source in 1000ml minimal salts medium in 7d at 55 degrees C. This strain was identified as Geobacillus kaustophilus by fatty acid methyl esters analysis and 16S rRNA full gene sequencing. G. kaustophilus TERI NSM showed 97% degradation of eicosane, 85% degradation of pentacosane and 77% degradation of triacontane in 10d when used as the carbon source. The strain TERI NSM could also degrade the paraffins of crude oil collected from oil wells that had a history of paraffin deposition problems.

Phytoremediation of shallow organically enriched marine sediments using benthic microalgae

We examined whether replantation of benthic microalgae (BMA) can remediate shallow organically enriched sediment. Nitzschia sp., the dominant species in the tested area (Hiroshima Bay, Japan), was isolated and mass cultured, then replanted in the same area. Changes in the condition of the sediment were monitored for five months. During the study period, we observed an increase in redox potential (ORP) and a decrease in acid-volatile sulfide (AVS) in the experimental area, indicating that the sediment condition changed from reduced to oxic. Organic matter in the sediment, represented by chemical oxygen demand (COD), ignition loss (IL) and organic nitrogen (ON) decreased significantly, while inorganic nutrients (ammonia and phosphate) increased in the interstitial water. These changes imply that oxygen produced by the replanted BMA may have enhanced aerobic bacterial activity, accelerating the decomposition of organic matter. Thus, replantation of BMA shows potential as a novel and promising "phytoremediation" method for organically enriched sediment.

Paenibacillus campinasensis BL11: a wood material-utilizing bacterial strain isolated from black liquor

In order to search for new thermophilic microorganisms and their enzymes, bacterial strains from black liquor of brownstock at washing stage of kraft pulping process were screened. Therein a multiple glycosyl hydrolase-producing strain, BL11, was isolated as a dominant species in the xylan-degrading bacterial population and identified as Paenibacillus campinasensis. The bacterial strain used all kinds of saccharides and polysaccharides, except lignin as carbon source and produced multiple extracellular polysaccharide-degrading enzymes, including one xylanase (41 kDa), three cellulases (42, 57 and 86 kDa), one pectinase (28 kDa) and one cyclodextrin glucanotransferase (38 kDa). P. campinasensis BL11 lacked lipase and protease activities and was able to grow over a wide range of pH, but it particularly grew well around neutral pH at 55 degrees C. Based on its physiological characteristics, it has strong potential for industrial application and bioresource utilization.

Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

BACKGROUND

Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78 degrees C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5-99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification.

RESULTS

Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70 degrees C and was also stable up to 60 degrees C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T).

CONCLUSION

Strain T1T was able to secrete extracellular thermostable lipase into culture medium. The strain T1T was identified as Geobacillus zalihae T1T as it differs from its type strains Geobacillus kaustophilus (DSM 7263T) and Geobacillus thermoleovorans (DSM 5366T) on some physiological studies, cellular fatty acids composition, RiboPrint analysis, length of lipase gene and protein profile.

Salinity-dependent switching of osmolyte strategies in a moderately halophilic bacterium: glutamate induces proline biosynthesis in Halobacillus halophilus

The moderately halophilic bacterium Halobacillus halophilus copes with the salinity in its environment by the production of compatible solutes. At intermediate salinities of around 1 M NaCl, cells produce glutamate and glutamine in a chloride-dependent manner (S. H. Saum, J. F. Sydow, P. Palm, F. Pfeiffer, D. Oesterhelt, and V. Müller, J. Bacteriol. 188:6808-6815, 2006). Here, we report that H. halophilus switches its osmolyte strategy and produces proline as the dominant solute at higher salinities (2 to 3 M NaCl). The proline biosynthesis genes proH, proJ, and proA were identified. They form a transcriptional unit and encode the pyrroline-5-carboxylate reductase, the glutamate-5-kinase, and the glutamate-5-semialdehyde dehydrogenase, respectively, catalyzing proline biosynthesis from glutamate. Expression of the genes was clearly salinity dependent and reached a maximum at 2.5 M NaCl, indicating that the pro operon is involved in salinity-induced proline biosynthesis. To address the role of anions in the process of pro gene activation and proline biosynthesis, we used a cell suspension system. Chloride salts lead to the highest accumulation of proline. Interestingly, chloride could be substituted to a large extent by glutamate salts. This unexpected finding was further analyzed on the transcriptional level. The cellular mRNA levels of all three pro genes were increased up to 90-fold in the presence of glutamate. A titration revealed that a minimal concentration of 0.2 M glutamate already stimulated pro gene expression. These data demonstrate that the solute glutamate is involved in the switch of osmolyte strategy from glutamate to proline as the dominant compatible solute during the transition from moderate to high salinity.

Glutamate restores growth but not motility in the absence of chloride in the moderate halophile Halobacillus halophilus

Halobacillus halophilus is a strictly chloride-dependent, moderately halophilic bacterium that synthesizes glutamate and glutamine as the major compatible solutes at intermediate NaCl concentrations. The key enzyme in production of the compatible solutes glutamine and glutamate, glutamine synthetase, is dependent on chloride on a transcriptional and activity level. This led us to ask whether exogenous supply of glutamate may relief the chloride dependence of growth of H. halophilus. Growth of H. halophilus in minimal medium at 1 M NaCl was stimulated by exogenous glutamate and transport experiments revealed a chloride-independent glutamate uptake by whole cells. Growth was largely impaired in the absence of chloride and, at the same time, glutamate and glutamine pools were reduced by 90%. Exogenous glutamate fully restored growth, and cellular glutamate and glutamine pools were refilled. Although glutamate could restore growth in the absence of chloride, another chloride-dependent process, flagellum synthesis and motility, was not restored by glutamate. The differential effect of glutamate on the two chloride-dependent processes, growth and motility, indicates that glutamate can not substitute chloride in general but apparently bypasses one function of the chloride regulon, the adjustment of pool sizes of compatible solutes.

Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov

Three strains of a spore-forming, Gram-positive, motile, rod-shaped and boron-tolerant bacterium were isolated from soil. The strains, designated 10aT, 11c and 12B, can tolerate 5 % (w/v) NaCl and up to 150 mM boron, but optimal growth was observed without addition of boron or NaCl in Luria–Bertani agar medium. The optimum temperature for growth was 37 °C (range 16–45 °C) and the optimum pH was 7.0–8.0 (range pH 5.5–9.5). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strains were closely related toBacillus fusiformisDSM 2898T(97.2 % similarity) andBacillus sphaericusDSM 28T(96.9 %). DNA–DNA relatedness was greater than 97 % among the isolated strains and 61.1 % withB. fusiformisDSM 2898Tand 43.2 % withB. sphaericusIAM 13420T. The phylogenetic and phenotypic analyses and DNA–DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5–37.9 mol%, MK-7 as the predominant menaquinone system and iso-C15 : 0(32 % of the total) as a major cellular fatty acid. In contrast to the type species of the genusBacillus, the strains contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid. Based on the distinctive peptidoglycan composition, phylogenetic analyses and physiology, the strains are assigned to a novel species within a new genus, for which the nameLysinibacillus boronitoleransgen. nov., sp. nov. is proposed. The type strain ofLysinibacillus boronitoleransis strain 10aT(=DSM 17140T=IAM 15262T=ATCC BAA-1146T). It is also proposed thatBacillus fusiformisandBacillus sphaericusbe transferred to this genus asLysinibacillus fusiformiscomb. nov. andLysinibacillus sphaericuscomb. nov., respectively.

Halophilic and halotolerant bacteria from river waters and shallow groundwater along the Rouge River of southeastern Michigan

The use of sodium chloride to melt highway and road snow is believed to have a significant effect on the groundwater ecosystem of the rivers where the salt from the roads drain. As the river composition changes, the bacterial population also changes to favour those bacteria that are more suited to the higher salt concentrations. In this experiment, we surveyed the cultivable salt-loving organisms (halophiles) on three sites that encompass the Rouge River (Lotz; site 1, Lilly, site; 8, and Ford Field, site 9). A total of 125 isolates were surveyed. Representative isolates of distinct morphologies were subjected to physiological test, using API strips and identified by 16 rDNA sequence analysis. The 16S rDNA sequences were analyzed and compared with sequences from Genbank. Results indicated that the SSU rRNA sequences of the bacterial isolates were similar to six major genera, Bacillus, Staphylococcus, Halobacillus, Paenabacillus, Halomonas, and Clostridium. Half of the isolates sequenced were similar to Bacillus spp. The API assay showed that the majority of the isolates were positive for the enzymes tryptophane deaminase, gelatinase and beta-galactosidase. Indole production, acetoin production and citrate utilization were not observed for any isolates. Fermentation of carbohydrates was observed for very few isolates. The primary enzyme found in all isolates was arginine dihydrolase, which might be an indicator of the presence of such enzyme in halophilic and halotolerant bacteria present in the Rouge River.

Desulfurispirillum alkaliphilum gen. nov. sp. nov., a novel obligately anaerobic sulfur- and dissimilatory nitrate-reducing bacterium from a full-scale sulfide-removing bioreactor

Strain SR 1(T)was isolated under anaerobic conditions using elemental sulfur as electron acceptor and acetate as carbon and energy source from the Thiopaq bioreactor in Eerbeek (The Netherlands), which is removing H(2)S from biogas by oxidation to elemental sulfur under oxygen-limiting and moderately haloalkaline conditions. The bacterium is obligately anaerobic, using elemental sulfur, nitrate and fumarate as electron acceptors. Elemental sulfur is reduced to sulfide through intermediate polysulfide, while nitrate is dissimilatory reduced to ammonium. Furthermore, in the presence of nitrate, strain SR 1(T) was able to oxidize limited amounts of sulfide to elemental sulfur during anaerobic growth with acetate. The new isolate is mesophilic and belongs to moderate haloalkaliphiles, with a pH range for growth (on acetate and nitrate) from 7.5 to 10.25 (optimum 9.0), and a salt range from 0.1 to 2.5 M Na(+) (optimum 0.4 M). According to phylogenetic analysis, SR 1(T) is a member of a deep bacterial lineage, distantly related to Chrysiogenes arsenatis (Macy et al. 1996). On the basis of the phenotypic and genetic data, the novel isolate is placed into a new genus and species, Desulfurispirillum alkaliphilum (type strain SR(T)= DSM 18275 = UNIQEM U250).

Geobacillus toebii subsp. decanicus subsp. nov., a hydrocarbon-degrading, heavy metal resistant bacterium from hot compost

A thermophilic, spore-forming bacterial strain L1(T) was isolated from hot compost "Pomigliano Environment" s.p.a., Pomigliano, Naples, Italy. The strain was identified by using a polyphasic taxonomic approach. L1(T) resulted in an aerobic, gram-positive, rod-shaped, thermophilic with an optimum growth temperature of 68 degrees C chemorganotrophic bacterium which grew on hydrocarbons as unique carbon and energy sources and was resistant to heavy metals. The G+C DNA content was 43.5 mol%. Phylogenetic analysis of 16S rRNA gene sequence and Random Amplified Polymorphic DNA-PCR (RAPD-PCR) analysis of L1(T) and related strains showed that it forms within Geobacillus toebii, a separate cluster in the Geobacillus genus. The composition of cellular fatty acids analyses by Gas-Mass Spectroscopy differed from that typical for the genus Geobacillus in that it is lacking in iso-C15 fatty acid, while iso-C16 and iso-C17 were predominant. Isolates grew on a rich complex medium at temperatures between 55-75 degrees C and presented a doubling time (t(d)) of 2 h and 6 h using complex media and hydrocarbon media, respectively. Among hydrocarbons tested, n-decane (2%) was the more effective to support the growth (1 g/L of wet cells). The microorganism showed resistance to heavy metal tested during the growth. Furthermore, intracellular alpha-galactosidase and alpha-glucosidase enzymatic activities were detectable in the L1(T) strain. Based on phenotypic, phylogenetic, fatty acid analysis and results from DNA-DNA hybridization, we propose assigning a novel subspecies of Geobacillus toebii, to be named Geobacillus toebii subsp. decanicus subsp. nov., with the type strain L1(T) (=DSM 17041=ATCC BAA 1004).

Solubilization, solution equilibria, and biodegradation of PAH's under thermophilic conditions

Biodegradation rates of PAHs are typically low at mesophilic conditions and it is believed that the kinetics of degradation is controlled by PAH solubility and mass transfer rates. Solubility tests were performed on phenanthrene, fluorene and fluoranthene at 20 degrees C, 40 degrees C and 60 degrees C and, as expected, a significant increase in the equilibrium solubility concentration and of the rate of dissolution of these polycyclic aromatic hydrocarbons (PAHs) was observed with increasing temperature. A first-order model was used to describe the PAH dissolution kinetics and the thermodynamic property changes associated with the dissolution process (enthalpy, entropy and Gibb's free energy of solution) were evaluated. Further, other relevant thermodynamic properties for these PAHs, including the activity coefficients at infinite dilution, Henry's law constants and octanol-water partition coefficients, were calculated in the temperature range 20-60 degrees C. In parallel with the dissolution studies, three thermophilic Geobacilli were isolated from compost that grew on phenanthrene at 60 degrees C and degraded the PAH more rapidly than other reported mesophiles. Our results show that while solubilization rates of PAHs are significantly enhanced at elevated temperatures, the biodegradation of PAHs under thermophilic conditions is likely mass transfer limited due to enhanced degradation rates.

Analysis of Protein Expression Profiles of Halobacillus dabanensis D-8T Under Optimal and High Salinity Conditions

Two-dimensional (2-D) gel electrophoresis was employed to display the expression profiles of proteins of Halobacillus dabanensis D-8(T) under 1%, 10%, and 20% salinities. Approximately 700 protein spots could be detected in the 2-D gels by Imagemastertrade mark 2D Platinum software. The molecular masses of the majority of intracellular proteins were distributed in the range of 17.5 kDa-66 kDa and isoelectric points of 4.0-5.9. In total 133 protein spots were observed with a changed expression level under different salinity conditions. Sixty-two protein spots showed upregulation and 26 new protein spots were found under high salinity conditions, while 25 protein spots were downregulated and 20 spots disappeared. Twenty-seven proteins with a markedly changed expression in hypersaline environments were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF/MS) and MASCOT. A changed expression pattern was observed for proteins related to energy-producing pathways, stress regulators, and proteins involved in the survival of strain D-8(T) under high salt challenges. Many proteins play necessary roles in the adaptation to high salt or as a general stress protein, and some proteins are salt-stressed specific proteins that improve the capability of salt-tolerance of strain D-8(T) growth under extremely hypersaline condition.

Multidimensional analysis of the insoluble sub-proteome ofOceanobacillus iheyensis HTE831, an alkaliphilic and halotolerant deep-sea bacterium isolated from the Iheya ridge

We report the first proteomic analysis of the insoluble sub-proteome of the alkaliphilic and halotolerant deep-sea bacterium Oceanobacillus iheyensis HTE831. A multidimensional gel-based and gel-free analysis was utilised and a total of 4352 peptides were initially identified by automated MS/MS identification software. Automated curation of this list using PROVALT reduced our peptide list to 467 uniquely identified peptides that resulted in the positive identification of 153 proteins. These identified proteins were functionally classified and physiochemically characterised. Of 26 proteins identified as hypothetical conserved, we have assigned function to all but four. A total of 41 proteins were predicted to possess signal peptides. In silico investigation of these proteins allowed us to identify three of the five bacterial classes of signal peptide, namely: (i) twin-arginine translocation; (ii) Sec-type and (iii) lipoprotein transport. Our proteomic strategy has also allowed us to identify, at neutral pH, a number of proteins described previously as belonging to two putative transport systems believed to be of importance in the alkaliphilic adaptation of O. iheyensis HTE831.

Cloning and characterization of the genes encoding a glycine betaine ABC-type transporter in Halobacillus trueperi DSM10404T

By using Southern blot hybridization and inverse polymerase chain reaction, a 5.5-kb DNA fragment was obtained from the genomic DNA of Halobacillus trueperi DSM10404(T). Sequence analysis revealed that it contained a potential operon with high levels of sequence similarity to the opuA operon encoding glycine betaine transporter from Bacillus subtilis, which is a member of the ATP-binding cassette (ABC) substrate binding the protein-dependent transporter superfamily. The potential operon, designated as qatA (quaternary amine transporter), consists of three structural genes, which are predicted to encode an ATP-binding protein (QatAA), a membrane-associated protein (QatAB), and an extracellular substrate-binding protein (QatAC). Moreover, the putative promoter region of the operon was found with close homology to the sigma(A)-dependent promoter of B. subtilis. Reverse transcription (RT)-PCR analysis revealed that qatAA, qatAB, and qatAC genes were transcribed in cells of H. trueperi. Cells of Escherichia coli mutant MKH13 harboring qatA on pAY41 were able to grow on selective M9 salt medium containing glycine betaine and accumulated glycine betaine in the cytoplasm, showing that qatAA, qatAB, and qatAC genes together encode a functional glycine betaine transporter.

Proteomic analysis of cold adaptation in a Siberian permafrost bacterium--Exiguobacterium sibiricum 255-15 by two-dimensional liquid separation coupled with mass spectrometry

Bacterial cold adaptation in Exiguobacterium sibiricum 255-15 was studied on a proteomic scale using a 2-D liquid phase separation coupled with MS technology. Whole-cell lysates of E. sibiricum 255-15 grown at 4 degrees C and 25 degrees C were first fractionated according to pI by chromatofocusing (CF), and further separated based on hydrophobicity by nonporous silica RP HPLC (NPS-RP-HPLC) which was on-line coupled with an ESI-TOF MS for intact protein M(r) measurement and quantitative interlysate comparison. Mass maps were created to visualize the differences in protein expression between different growth temperatures. The differentially expressed proteins were then identified by PMF using a MALDI-TOF MS and peptide sequencing by MS/MS with a MALDI quadrupole IT TOF mass spectrometer (MALDI-QIT-TOF MS). A total of over 500 proteins were detected in this study, of which 256 were identified. Among these proteins 39 were cold acclimation proteins (Caps) that were preferentially or uniquely expressed at 4 degrees C and three were homologous cold shock proteins (Csps). The homologous Csps were found to be similarly expressed at 4 degrees C and 25 degrees C, where these three homologous Csps represent about 10% of the total soluble proteins at both 4 degrees C and 25 degrees C.

A two-component system regulates the expression of an ABC transporter for xylo-oligosaccharides in Geobacillus stearothermophilus

Geobacillus stearothermophilus T-6 utilizes an extensive and highly regulated hemicellulolytic system. The genes comprising the xylanolytic system are clustered in a 39.7-kb chromosomal segment. This segment contains a 6-kb transcriptional unit (xynDCEFG) coding for a potential two-component system (xynDC) and an ATP-binding cassette (ABC) transport system (xynEFG). The xynD promoter region contains a 16-bp inverted repeat resembling the operator site for the xylose repressor, XylR. XylR was found to bind specifically to this sequence, and binding was efficiently prevented in vitro in the presence of xylose. The ABC transport system was shown to comprise an operon of three genes (xynEFG) that is transcribed from its own promoter. The nonphosphorylated fused response regulator, His6-XynC, bound to a 220-bp fragment corresponding to the xynE operator. DNase I footprinting analysis showed four protected zones that cover the -53 and the +34 regions and revealed direct repeat sequences of a GAAA-like motif. In vitro transcriptional assays and quantitative reverse transcription-PCR demonstrated that xynE transcription is activated 140-fold in the presence of 1.5 microM XynC. The His6-tagged sugar-binding lipoprotein (XynE) of the ABC transporter interacted with different xylosaccharides, as demonstrated by isothermal titration calorimetry. The change in the heat capacity of binding (DeltaCp) for XynE with xylotriose suggests a stacking interaction in the binding site that can be provided by a single Trp residue and a sugar moiety. Taken together, our data show that XynEFG constitutes an ABC transport system for xylo-oligosaccharides and that its transcription is negatively regulated by XylR and activated by the response regulator XynC, which is part of a two-component sensing system.

Autoinducer-2-producing protein LuxS, a novel salt- and chloride-induced protein in the moderately halophilic bacterium Halobacillus halophilus

The moderately halophilic bacterium Halobacillus halophilus carries a homologue of LuxS, a protein involved in the activated methyl cycle and the production of autoinducer-2, which mediates quorum sensing between certain species. luxS of H. halophilus is part of an operon that encodes an S-adenosylmethionine-dependent methyltransferase, a cysteine synthase, and a beta-cystathionine lyase. Expression of luxS was growth phase dependent, with maximal expression in the mid-exponential growth phase. In addition, transcription of luxS was strictly salt dependent; maximal mRNA concentrations were observed with 2.0 M NaCl in the growth medium. Chloride ions stimulated luxS transcription by a factor of three. Western blot analyses demonstrated a growth phase- and salinity-dependent production of LuxS. Moreover, cellular LuxS levels were strictly chloride dependent. Maximal accumulation of LuxS was observed at 0.5 to 1.0 M Cl(-) and depended on the salinity.

Biochemical and molecular characterization of the biosynthesis of glutamine and glutamate, two major compatible solutes in the moderately halophilic bacterium Halobacillus halophilus

The moderately halophilic, chloride-dependent bacterium Halobacillus halophilus produces glutamate and glutamine as main compatible solutes at external salinities of 1.0 to 1.5 M NaCl. The routes for the biosynthesis of these solutes and their regulation were examined. The genome contains two genes potentially encoding glutamate dehydrogenases and two genes for the small subunit of a glutamate synthase, but only one gene for the large subunit. However, the expression of these genes was not salt dependent, nor were the corresponding enzymatic activities detectable in cell extracts of cells grown at different salinities. In contrast, glutamine synthetase activity was readily detectable in H. halophilus. Induction of glutamine synthetase activity was strictly salt dependent and reached a maximum at 3.0 M NaCl; chloride stimulated the production of active enzyme by about 300%. Two potential genes encoding a glutamine synthetase, glnA1 and glnA2, were identified. The expression of glnA2 but not of glnA1 was increased up to fourfold in cells adapted to high salt, indicating that GlnA2 is the glutamine synthetase involved in the synthesis of the solutes glutamate and glutamine. Furthermore, expression of glnA2 was stimulated twofold by the presence of chloride ions. Chloride exerted an even more pronounced effect on the enzymatic activity of preformed enzyme: in the absence of chloride in the assay buffer, glutamine synthetase activity was decreased by as much as 90%. These data demonstrate for the first time a regulatory role of a component of common salt, chloride, in the biosynthesis of compatible solutes.