Rapid and sensitive NMR method for osmolyte determination

Microbial Remediation of Crude Oil in Saline Conditions by Oil-Degrading Bacterium Priestia megaterium FDU301

Salinity greatly affects the microbial degradation process of crude oil; thus, the isolation and identification of halotolerant microbes is essential. Limited studies explored how microbes respond to increased salinity. In this study, an oil-degrading bacterium Priestia megaterium FDU301 was isolated from the Dagang oil field, which can tolerate a salinity of 6%. Compared to the non-saline condition, oil degradation ratios by P. megaterium FDU301 increased by 15.27% and 11.26% in 0.5% and 3.5% salinity media, respectively. Meanwhile, bacteria degraded various components of crude oil more thoroughly in saline environments, especially mid-chain hydrocarbons (C11-C18). Surface tension under salt stress was lower than that in the non-saline medium, indicating that the amount of biosurfactants produced by bacteria was increased. The microbial activity enhanced markedly in response to increased salinity, which was the main factor for the high degradation ability. As a vital component of biofilms, the production of polysaccharides was accelerated with P. megaterium FDU301 inoculation in saline environments. These results indicate that P. megaterium FDU301 has great potential application in oil bioremediation in saline environments.

Salinity Tolerance and Osmoadaptation Strategies in Four Genera of Anammox Bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua

The salinity tolerance and osmoadaptation strategies in four phylogenetically distant anammox species, Brocadia, Jettenia, Kuenenia, and Scalindua, were investigated by using highly enriched cell cultures. The first-emerged "Ca. Scalindua sp." showed optimum growth at 1.5-3% salinity and was tolerant to ∼10% salinity (a slight halophile). The second-emerged "Ca. Kuenenia stuttgartiensis" was tolerant to ∼6% salinity with optimum growth at 0.25-1.5% (a halotolerant). These early-emerged "Ca. Scalindua sp." and ″Ca. K. stuttgartiensis" rapidly accumulated K+ ions and simultaneously synthesized glutamate as a counterion. Subsequently, part of the glutamate was replaced by trehalose. In contrast, the late-emerged "Ca. B. sinica" and "Ca. J. caeni" were unable to accumulate sufficient amounts of K+─glutamate and trehalose, resulting in a significant decrease in activity even at 1-2% salinity (nonhalophiles). In addition, the external addition of glutamate may increase anammox activity at high salinity. The species-dependent salinity tolerance and osmoadaptation strategies were consistent with the genetic potential required for the biosynthesis and transport of these osmolytes and the evolutionary history of anammox bacteria: Scalindua first emerged in marine environments and then Kuenenia and other two species gradually expanded their habitat to estuaries, freshwater, and terrestrial environments, while Brocadia and Jettenia likely lost their ability to accumulate K+─glutamate.

The saltern-derived Paludifilum halophilum DSM 102817T is a new high-yield ectoines producer in minimal medium and under salt stress conditions

In the present study, the growth conditions and accumulation of ectoines (ectoine and hydroxyectoine) by Paludifilum halophilum DSM 102817^T under salt stress conditions have been investigated. The productivity assay of this strain for ectoines revealed that the highest cellular content was reached in the minimal glucose sea water medium (SW-15) within 15% salinity. The addition of 0.1% (w/v) aspartic acid to the medium allowed an average of four times higher biomass production, and a dry mycelial biomass of 1.76 g L^-1 was obtained after 6 days of growth in shake flasks at 40 °C and 200 rpm. Among the inorganic cations supplemented to the glucose SW-15 medium, the addition of 1 mM Fe²⁺ yielded the highest amount of mycelial biomass (3.45 g L^-1) and total ectoines content (119 mg g^-1), resulting in about 410 mg L^-1 of products at the end of exponential growth phase. After 1 h of incubation in an osmotic downshock solution containing 2% NaCl, 70% of this content was released by the mycelium, and recovering cells maintained a high survival, with a maximal growth rate (µ _max) of about 93% of the control population exposed to 15% NaCl. During growth at optimal salinity and temperature (15% NaCl and 40 °C), P. halophilum developed a compact and circular pellets that were easy to separate by simple decantation from both fermentation media and after hypoosmotic shock. Overall, the ectoines excreting P. halophilum could be a promising resource for ectoines production in a commercially valuable culture medium and at a large-scale fermentation process.

Determination of Intracellular Osmolytes in Cyanobacterial Cells

Most of the cyanobacteria accumulate osmolytes including sucrose, glucosylglycerol, in their cells in response to salt stress. Here we describe a protocol of our laboratory for extraction and quantification of cyanobacterial intracellular sucrose and glucosylglycerol. We have confirmed this protocol was applicable to at least four kinds of cyanobacteria, filamentous cyanobacterium Anabaena sp. PCC 7120, unicellular cyanobacterium Synechocystis sp. PCC 6803, Synechococcus elongatus PCC 7942 and halotolerant unicellular cyanobacterium Synechococcus sp. PCC 7002.

Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress

The moderately halophilic bacterium Virgibacillus halodenitrificans PDB-F2 copes with salinity by synthesizing or taking up compatible solutes. The main compatible solutes in this strain were ectoine and hydroxyectoine, as determined by (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR). A high-performance liquid chromatography (HPLC) analysis showed that ectoine was the major solute that was synthesized in response to elevated salinity, while hydroxyectoine was a minor solute. However, the hydroxyectoine/ectoine ratio increased from 0.04 at 3 % NaCl to 0.45 at 15 % NaCl in the late exponential growth phase. A cluster of ectoine biosynthesis genes was identified, including three genes in the order of ectA, ectB, and ectC. The hydroxyectoine biosynthesis gene ectD was not part of the ectABC gene cluster. Reverse transcription-quantitative polymerase chain reactions (RT-qPCR) showed that the expression of the ect genes was salinity dependent. The expression of ectABC reached a maximum at 12 % NaCl, while ectD expression increased up to 15 % NaCl. Ectoine and hydroxyectoine production was growth phase dependent. The hydroxyectoine/ectoine ratio increased from 0.018 in the early exponential phase to 0.11 in the stationary phase at 5 % NaCl. Hydroxyectoine biosynthesis started much later than ectoine biosynthesis after osmotic shock, and the temporal expression of the ect genes differed under these conditions, with the ectABC genes being expressed first, followed by ectD gene. Increased culture salinity triggered ectoine or hydroxyectoine uptake when they were added to the medium. Hydroxyectoine was accumulated preferentially when both ectoine and hydroxyectoine were provided exogenously.

Biodegradation of benzene homologues in contaminated sediment of the East China Sea

This study focused on acclimating a microbial enrichment to biodegrade benzene, toluene, ethylbenzene and xylenes (BTEX) in a wide range of salinity. The enrichment degraded 120 mg/L toluene within 5d in the presence of 2M NaCl or 150 mg/L toluene within 7d in the presence of 1-1.5M NaCl. PCR-DGGE (polymerase chain reaction-denatured gradient gel electrophoresis) profiles demonstrated the dominant species in the enrichments distributed between five main phyla: Gammaproteobacteria, Sphingobacteriia, Prolixibacter, Flavobacteriia and Firmicutes. The Marinobacter, Prolixibacter, Balneola, Zunongwangia, Halobacillus were the dominant genus. PCR detection of genotypes involved in bacterial BETX degradation revealed that the degradation pathways contained all the known initial oxidative attack of BTEX by monooxygenase and dioxygenase. And the subsequent ring fission was catalysed by catechol 1,2-dioxygenase and catechol 2,3-dioxygenase. Nuclear magnetic resonance (NMR) spectroscopy profiles showed that the bacterial consortium adjusted the osmotic pressure by ectoine and hydroxyectoine as compatible solutes to acclimate the different salinity conditions.

Rrp4 and Csl4 are needed for efficient degradation but not for polyadenylation of synthetic and natural RNA by the archaeal exosome

The exosome of the archaeon Sulfolobus solfataricus is a protein complex with phosphorolytic and polyadenylating activity. Little is known about its substrates and the regulation of its functions. We characterized the catalytically active hexameric ring composed of SsoRrp41 and SsoRrp42, and the nine-subunit exosomes containing in addition RNA binding protein SsoRrp4 or SsoCsl4 under various reaction conditions. The exosome synthesized heteropolymeric RNA tails and exhibited the highest in vitro activity at 60-70 degrees C. MgCl(2) was necessary for exosome activity. The two reactions, degradation and polyadenylation of RNA, were inhibited by increasing glycerol and KCl concentrations but were differently influenced by changes in pH and by increasing MgCl(2) concentrations. The three protein complexes with different compositions were similarly influenced by increasing concentrations of glycerol, KCl, and MgCl(2), but the SsoRrp4 exosome behaved differently with respect to pH changes. A 20-nucleotide poly(A) tail enabled the degradation and the polyadenylation of a 16S rRNA-derived transcript by the hexamer. Generally, RNA synthesis by the hexamer was more efficient than RNA phosphorolysis. Single-stranded poly(A) RNA, a heteropolymeric 97-nucleotide transcript, and natural tRNA were quickly polyadenylated, showing that these substrates were bound and their 3'-ends reached the active site. Despite this, their efficient degradation was possible only in the presence of SsoRrp4 or SsoCsl4. Thus, strong substrate binding by SsoRrp4- or SsoCsl4-containing exosomes is more important for phosphorolysis than for tailing of RNA. In summary, the data suggest that subunit composition and Mg(2+) are involved in the regulation of exosome activity.

Halomonas sinaiensis sp. nov., a novel halophilic bacterium isolated from a salt lake inside Ras Muhammad Park, Egypt

An alkalitolerant and halotolerant bacterium, designated strain Sharm was isolated from a salt lake inside Ras Muhammad. The morphological, physiological and genetic characteristics were compared with those of related species of the genus Halomonas. The isolate grew optimally at pH 7.0, 5-15% NaCl at 35 degrees C. The cells were Gram-negative rods, facultative anaerobes. They accumulated glycine-betaine, as a major osmolyte, and ectoine and glutamate as minor components. The strain Sharm(T) biosynthetised alpha-glucosidase. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and a novel phosphoglycolipid as major components. Ubiquinone with nine repetitive unities (Q9) was the only quinone found and, nC16:0 and C19:0 with cyclopropane were the main cellular fatty acids, accounting for 87.3% of total fatty acids. The G + C content of the genomic DNA was 64.7 mol %. The 16S rRNA sequence analysis indicated that strain Sharm was a member of the genus Halomonas. The closest relatives of the strain Sharm were Halomonas elongata and Halomonas eurihalina. However, DNA-DNA hybridisation results clearly indicated that strain Sham was a distinct species of Halomonas. On the basis of the evidence, we propose to assign strain Sharm as a new species of the genus Halomonas, H. sinaiensis sp. nov, with strain Sharm(T) as the type strain (DSM 18067(T); ATCC BAA-1308(T)).

Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain

An extremely halophilic archaeon belonging to the order Halobacteriales was isolated from Fuente de Piedra salt lake, Spain. This strain, designated FP1T, was a pleomorphic coccoid, neutrophilic and required at least 15 % (w/v) NaCl for growth. Strain FP1T grew at 37–60 °C, with optimal growth at 50 °C. Mg2+ was not required, but growth was observed with up to 10 % (w/v) MgSO4. Polar lipid analysis revealed the presence of mannose-6-sulfate(1-2)-glucose glycerol diether as a major glycolipid. Both C20C20 and C20C25 core lipids were present. The genomic DNA G+C content was 62.0 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was most closely related to species of the genus Haloterrigena. DNA–DNA reassociation values between strain FP1T and the most closely related species of the genus Haloterrigena (Haloterrigena thermotolerans, Haloterrigena saccharevitans and Haloterrigena limicola) were lower than 29 %. It is therefore considered that strain FP1T represents a novel species of the genus Haloterrigena, for which the name Haloterrigena hispanica sp. nov. is proposed. The type strain is FP1T (=DSM 18328T=ATCC BAA-1310T).

Bacterial osmosensing transporters

Cells faced with dehydration because of increasing extracellular osmotic pressure accumulate solutes through synthesis or transport. Water follows, restoring cellular hydration and volume. Prokaryotes and eukaryotes possess arrays of osmoregulatory genes and enzymes that are responsible for solute accumulation under osmotic stress. In bacteria, osmosensing transporters can detect increasing extracellular osmotic pressure and respond by mediating the uptake of organic osmolytes compatible with cellular functions ("compatible solutes"). This chapter reviews concepts and methods critical to the identification and study of osmosensing transporters. Like some experimental media, cytoplasm is a "nonideal" solution so the estimation of key solution properties (osmotic pressure, osmolality, water activity, osmolarity, and macromolecular crowding) is essential for studies of osmosensing and osmoregulation. Because bacteria vary widely in osmotolerance, techniques for its characterization provide an essential context for the elucidation of osmosensory and osmoregulatory mechanisms. Powerful genetic, molecular biological, and biochemical tools are now available to aid in the identification and characterization of osmosensory transporters, the genes that encode them, and the osmoprotectants that are their substrates. Our current understanding of osmosensory mechanisms is based on measurements of osmosensory transporter activity performed with intact cells, bacterial membrane vesicles, and proteoliposomes reconstituted with purified transporters. In the quest to elucidate the structural mechanisms of osmosensing and osmoregulation, researchers are now applying the full range of available biophysical, biochemical, and molecular biological tools to osmosensory transporter prototypes.

Oceanobacillus oncorhynchi subsp. incaldanensis subsp. nov., an alkalitolerant halophile isolated from an algal mat collected from a sulfurous spring in Campania (Italy), and emended description of Oceanobacillus oncorhynchi

A halophilic, alkalitolerant bacterium, strain 20AGT, was isolated from an algal mat collected from a sulfurous spring located in Santa Maria Incaldana (Mondragone, Campania Region, southern Italy). The isolate is Gram-positive, ferments several carbohydrates and has motile, rod-shaped cells that do not sporulate. The isolate grows at pH 6.5-9.5 and in 5-20 % NaCl. On the basis of 16S rRNA gene sequence similarity, the strain was shown to belong to the genus Oceanobacillus; strain 20AGT showed 96.6 % 16S rRNA gene sequence similarity to the type strain of Oceanobacillus iheyensis, DSM 14371T, and 99.5 % similarity to Oceanobacillus oncorhynchi NCIMB 14022T. Levels of DNA-DNA relatedness between strain 20AGT and O. iheyensis DSM 14371T and O. oncorhynchi NCIMB 14022T were respectively 29.4 and 59.0 %. The G+C content of the DNA of strain 20AGT was 40.1 mol%. The predominant respiratory quinone was MK-7, phosphatidylglycerol and phosphatidylcholine were the predominant polar lipids and minor phospholipids were also detected. ai-C14 : 0, ai-C15 : 0 and i-C15 : 0 were the major fatty acids. Strain 20AGT accumulated osmolytes and produced exopolysaccharide. On the basis of phenotypic characteristics, phylogenetic data and DNA-DNA relatedness data, isolate 20AGT should be designated as the type strain of a subspecies of Oceanobacillus oncorhynchi, for which the name Oceanobacillus oncorhynchi subsp incaldanensis subsp. nov. is proposed. The type strain is 20AGT (=DSM 16557T = ATCC BAA-954T).

Levels of glycine betaine in growing cells and spores of Bacillus species and lack of effect of glycine betaine on dormant spore resistance

Bacteria of various Bacillus species are able to grow in media with very high osmotic strength in part due to the accumulation of low-molecular-weight osmolytes such as glycine betaine (GB). Cells of Bacillus species grown in rich and minimal media contained low levels of GB, but GB levels were 4- to 60-fold higher in cells grown in media with high salt. GB levels in Bacillus subtilis cells grown in minimal medium were increased approximately 7-fold by GB in the medium and 60-fold by GB plus high salt. GB was present in spores of Bacillus species prepared in media with or without high salt but at lower levels than in comparable growing cells. With spores prepared in media with high salt, GB levels were highest in B. subtilis spores and > or =20-fold lower in B. cereus and B. megaterium spores. Although GB levels in B. subtilis spores were elevated 15- to 30-fold by GB plus high salt in sporulation media, GB levels did not affect spore resistance. GB levels were similar in wild-type B. subtilis spores and spores that lacked major small, acid-soluble spore proteins but were much lower in spores that lacked dipicolinic acid.

Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy)

A halotolerant and alkaliphilic Gram-negative bacterium, strain 18bAG(T), that grows aerobically at the optimum temperature of 37 degrees C, and at pH 7.5-10 (optimum 9.0), was isolated from a salt pool located in Montefredane in Campania Region (South of Italy). The isolate tolerated high concentration of NaCl up to 20%. Strain 18bAG(T) accumulated osmolytes and polyhydroxybutyrate, produced exopolysaccharide and possessed alpha-glucosidase activity. The predominant respiratory quinones were ubiquinones, Q8 and Q6(6H); phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. Major fatty acids were C16 : 1, C16 : 0, and C18 : 0. On the basis of 16S rRNA gene sequence similarity, 18bAG(T) was shown to belong to Halomonas genus. Analysis of 16S rRNA gene revealed a high similarity of strain 18bAG(T) to Halomonas venusta (DSM 4743(T)) and Halomonas hydrothermalis (DSM 15725(T)). Level of DNA-DNA relatedness between strain 18bAG(T) and the most related species Halomonas venusta and Halomonas hydrothermalis was 56.0% and 41.2%, respectively. The G+C content (mol%) of DNA was 53.0. The RiboPrinting patterns of Halomonas venusta and 18AG(T) showed a pattern similarity of 0.50. On the basis of genomic information and phenotypic characteristics strain 18bAG(T) represents a new species, for which the name Halomonas alkaliphila sp. nov. is proposed. The type strain is 18bAG(T) (=DSM 16354T =ATCC BAA-953T).

Organic compatible solutes of halotolerant and halophilic microorganisms

Microorganisms that adapt to moderate and high salt environments use a variety of solutes, organic and inorganic, to counter external osmotic pressure. The organic solutes can be zwitterionic, noncharged, or anionic (along with an inorganic cation such as K(+)). The range of solutes, their diverse biosynthetic pathways, and physical properties of the solutes that effect molecular stability are reviewed.

Salinivibrio costicola subsp. alcaliphilus subsp. nov., a haloalkaliphilic aerobe from Campania Region (Italy)

Phenotypic and phylogenetic studies were performed on unidentified Gram-negative staining, haloalkaliphilic aerobe and protease producer Salinivibrio-like organism recovered from a saltish spring with algal mat in the "Pozzo del Sale" site (Salt's Well) in the Campania Region (South Italy). Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was related to species of Salinivibrio genus. The DNA-DNA hybridization of the type strain 18AG(T) with the most related Salinivibrio costicola subsp. costicola showed a reassociation value of 72%. Based on the phenotypic distinctiveness of 18AG(T) strain and molecular, chemical and genetic evidence, it is proposed that strain 18AG(T) can be classified as S. costicola subsp. alcaliphilus, subsp. nov. The type strain of S. costicola subsp. alcaliphilus, is ATCC BAA-952(T); DSM 16359(T).