Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study

So far only little is known about the microbial ecology of Mediterranean deep-sea hypersaline anoxic lakes (DHALs). These brine lakes were formed by evaporite dissolution/brine seeps and are important model environments to provide insights into possible metabolisms and distributions of microorganisms on the early Earth. Our study on the Lake Thetis, a new thalassohaline DHAL located South-East of the Medriff Corridor, has revealed microbial communities of contrasting compositions with a high number of novel prokaryotic candidate divisions. The major finding of our present work is co-occurrence of at least three autotrophic carbon dioxide fixation pathways in the brine-seawater interface that are likely fuelled by an active ramified sulphur cycle. Genes for the reductive acetyl-CoA and reductive TCA pathways were also found in the brine suggesting that these pathways are operational even at extremely elevated salinities and that autotrophy is more important in hypersaline environments than previously assumed. Surprisingly, genes coding for RuBisCo were found in the highly reduced brine. Three types of sulphide oxidation pathways were found in the interface. The first involves a multienzyme Sox complex catalysing the complete oxidation of reduced sulphur compounds to sulphate, the second type recruits SQR sulphide:quinone reductase for oxidation of sulphide to elemental sulphur, which, in the presence of sulphide, could further be reduced by polysulphide reductases in the third pathway. The presence of the latter two allows a maximal energy yield from the oxidation of sulphide and at the same time prevents the acidification and the accumulation of S(0) deposits. Amino acid composition analysis of deduced proteins revealed a significant overrepresentation of acidic residues in the brine compared with the interface. This trait is typical for halophilic organisms as an adaptation to the brine's extreme hypersalinity. This work presents the first metagenomic survey of the microbial communities of the recently discovered Lake Thetis whose brine constitutes one of saltiest water bodies ever reported.     

Bacterial and chemical leaching pattern on copper ores of sandstone and limestone type

Thin polished sections of copper sulphide ore were placed as an energy source in stationary cultures of wild strains and Thiobacillus neapolitanus at pH 7.5. Scanning electron microscopy revealed characteristic leaching patterns that depended on the type of leaching process and time of bioleaching. In some cases, a biological film on the ore surface was observed. Close contact between bacterial cells and ore seems necessary for leaching in some cases.M. Ostrowski and A. Skodowska are with the Department of Photo and Image Information, University of Warsaw, ul.Nowy wiat 67, 00-046 Warsaw, Poland.     

Cell permeability as a rate limiting factor in the microbial reduction of sulfonated azo dyes

Summary Permeabilization of cells of B. cereus and other bacterial strains by toluene treatment significantly increased the passage of sulfonated and carboxylated azo dyes from the external medium into the cells with a concomittant increase of the reduction rate of the dyes. Dyes which are not reduced at all by intact cells were readily decolorized. The reduction rate of sulfonated compounds was consistently larger than of their carboxylated analogues, once the dyes had entered the cells.     

Sulphur metabolism in Thiorhodaceae. II. stoichiometric relationship of CO2 fixation to oxidation of hydrogen sulphide and intracellular sulphur inChromatium okenii

Stoichiometry of sulphide and intracellular sulphur oxidation in connection with CO₂ fixation was studied inChromatium okenii. The equipment used was a special stirred cuvette with a rapid-sampling arrangement, which allowed short-time experiments with illuminated bacterial suspensions under anaerobic conditions. Turnover of the sulphur compounds is controlled by a linear CO₂ fixation rate which amounts to 0.069µmoles of CO₂/min mg of cell protein at light saturation. Van Niel's equations for bacterial photosynthesis could be confirmed for short periods under the condition that sulphate is produced during increase of intracellular sulphur; i.e., oxidation of sulphide and of intracellular sulphur do not occur consecutively but simultaneously. The full oxidation rate of intracellular sulphur starts after complete consumption of sulphide. The time during which sulphide is oxidized to intracellular sulphur amounts to 1/3–1/4 of the time necessary for the complete quantitative oxidation of the sulphide to sulphate.     

The electrochemical proton potential generated by the sulphur respiration of Wolinella succinogenes

Wolinella succinogenes grown on formate and elemental sulphur was found to use the polysulphide derivatives 2,2-tetrathiobispropionate (R₂S₄) or pentathionate (S₅O ₆ ⁼ ) as acceptors for formate oxidation. The specific activities of formate oxidation with these acceptors were similar to those with elemental sulphur. The main reaction products of R₂S₄ reduction were 2,2-dithiobispropionate (R₂S₂) and sulphide. Pentathionate was converted to thiosulphate and some elemental sulphur. The electrochemical proton potential across the cytoplasmic membrane of the bacterium was measured in the steady state of electron transport from formate to R₂S₄. The electrical proportion () of the determined through the distribution of labeled tetraphenylphosphonium cation was obtained as 0.17 Volt. The was zero, when a protonophore was present. The pH-difference across the membrane was negligible. Thus the generated by sulphur respiration is close to that measured earlier with fumarate as the terminal acceptor of electron transport.Abbreviations DMO 5,5-dimethyloxazolidine-2,4-dione - R₂S_n (n=2–5) 2,2-polythiobispropionate - TTFB 4,5,6,7-tetrachloro-2-trifluoromethylbenzimidazol - TPP tetraphenylphosphonium cation     

Substrate level versus oxidative phosphorylation in the generation of ATP in Thiobacillus denitrificans

Particulate fractions of Thiobacillus denitrificans catalyse the phosphorylation of ADP to ATP during the oxidation of various inorganic sulphur compounds or NADH via an electron transport chain. On the other hand, a soluble cell-free fraction synthesized ATP from APS and inorganic phosphate.The production of ATP was verified either by the firefly luciferin-luciferase enzyme system or by the incorporation of ³²Pi into ATP. During the oxidation of sulphide, sulphite and NADH the production of ATP from ADP by particulate fractions is inhibited by compounds that inhibit electron transfer and by uncouplers of oxidative phosphorylation. However, these compounds had little effect on the production of ATP from AMP during the oxidation of sulphite by the soluble fraction. NADH was the most effective electron donor for oxidative phosphorylation. The soluble fraction contained high activities of ATP sulphurylase, inorganic pyrophosphatase and adenylate kinase but ADP sulphurylase activity was relatively low. The effects of inhibitors on ATP production from APS and Pi are compared with those on adenylate kinase and ATP sulphurylase.Abbreviations APS adenosine-5-phosphosulphate - DNP 2,4-dinitrophenol - HOQNO 2-n-heptyl-4-hydroxyquinoline-N-oxide     

Glutamine metabolism in AS-30D hepatoma cells. Evidence for its conversion into lipids via reductive carboxylation

A study was undertaken to assess the role of a physiological concentration of glutamine in AS-30D cell metabolism. Flux of¹⁴C-glutamine to¹⁴CO₂ and of¹⁴C-acetate to glutamate was detected indicating reversible flux between glutamate and TCA cycle -ketoglutarate. These fluxes were transaminase dependent. A flux analysis was compared using data from three tracers that label -ketoglutarate carbon 5, [2-¹⁴C]glucose, [1-¹⁴C]acetate and [5-¹⁴C]glutamine. The analysis indicated that the probability of flux of TCA cycle -ketoglutarate to glutamate was, at minimum, only slightly less than the probability of flux of -ketoglutarate through -ketoglutarate dehydrogenase. The apparent Km for oxidative flux of [¹⁴C]glutamine to¹⁴CO₂, 0.07 mM, indicated that this flux was at a maximal rate at physiological, 0.75 mM, glutamine. Although oxidative flux through -ketoglutarate dehydrogenase was the major fate of glutamine, flux of glutamine to lipid via reductive carboxylation of -ketoglutarate was demonstrated by measuring incorporation of [5-¹⁴C]glutamine into¹⁴C-lipid. In media containing glucose (6 mM), and glutamine (0.75 mM) 47 per cent of the lipid synthesized from substrates in the media was derived from glutamine via reductive carboxylation and 49 per cent from glucose. These findings of nearly equal fluxes suggest that lipogenesis via reductive carboxylation may be an important role of glutamine in hepatoma cells.     

Desulphuring of natural gas and petroleum oil by autotrophic Thiobacillus ferrooxidans

Hydrogen sulphide is a common toxic contaminant in natural gas and oil. In this study, the strictly autotrophic bacterium Thiobacillus ferrooxidans , which oxidizes reduced sulphur compounds, was used to desulphur petroleum oil and gas. The reaction was carried out in a closed vessel containing substrate mixed with a bacterial suspension. The significance of the hydrogen sulphide oxidizing activity of T. ferrooxidans is discussed.     

Lethality and mutagenicity inHalobacterium mediterranei caused by N-methyl-N′-nitro-N-nitrosoguanidine

Compared withEscherichia coli, Halobacterium mediterranei was highly resistant to the lethal effect of N-methyl-N-nitro-N-nitrosoguanidine (nitrosoguanidine), but it was sensitive to the mutagenic action of this chemical agent. Nitrosoguanidine at 500 g ml^–1 gave a cell survival level between 1% and 10%, and this allowed us to obtain more Josamycin-resistant mutants compared with lower concentrations, which gave higher survival rates but fewer mutants. The efficiency of the mutagenicity obtained with the nitrosoguanidine treatment was examined under a variety of conditions. The optimal conditions for obtaining Josamycinresistant mutants were achieved by exposing, in darkness and without shaking, a suspension of about 10⁸ log-phase cells to 500 g nitrosoguanidine in 1 ml of 50 mM modified saline Tris-maleate buffer at pH 7.5, or in 1 ml of 5 mM modified saline Tris-citrate-maleate for 30 min at 37°C.     

Regulation of anaerobic respiratory pathways in Wolinella succinogenes by the presence of electron acceptors

In Wolinella succinogenes ATP synthesis and consequently bacterial growth can be driven by the reduction of either nitrate (E₀=+0.42 V), nitrite (E₀=+0.36 V), fumarate (E₀=+0.03 V) or sulphur (E₀=-0.27 V) with formate as the electron donor. Bacteria growing in the presence of nitrate and fumarate were found to reduce both acceptors simultaneously, while the reduction of both nitrate and fumarate is blocked during growth with sulphur. These observations were paralleled by the presence and absence of the corresponding bacterial reductase activities. Using a specific antiserum, fumarate reductase was shown to be present in bacteria grown with fumarate and nitrate, and to be nearly absent from bacteria grown in the presence of sulphur. The contents of polysulphide reductase, too, corresponded to the enzyme activities found in the bacteria. This suggests that the activities of anaerobic respiration are regulated at the biosynthetic level in W. succinogenes. Thus nitrate and fumarate reduction are repressed by the most electronegative acceptor of anacrobic respiration, sulphur. By contrast, in Escherichia coli a similar effect is exerted by the most electropositive acceptor, O₂. W. succinogenes also differs from E. coli in that fumarate reductase is not repressed by nitrate.Abbreviations BV benzyl viologen - DMN 2,3-dimethyl-1,4-naphthoquinone - DMSO dimethylsulfoxide - TMAO trimethylamine-N-oxide     

Dependence of effectiveness of leaching of metallic sulphides on enzymes involved in inorganic sulphur metabolism in Thiobacillus ferrooxidans

Summary The leaching activity of five batches of Thiobacillus ferrooxidans, strain F26-77, cultivated under various conditions, towards elemental sulphur, ferrous ions, pyrite, covellite, chalcopyrite and sphalerite was studied. The activities of sulphite oxidase, thiosulphate oxidase and rhodanese were determined in crude, cell-free bacterial extracts. The effectiveness of leaching was directly correlated with the enzymic activity of the cultures. The results suggest that the activities of the enzymes metabolizing sulphur and its inorganic compounds in Thiobacillus ferrooxidans, or bacterial leaching activity on sulphur and sulphides, rather than the rate of oxidation of ferrous ions, should be taken as the criterion of usefulness for the leaching of sulphide minerals.     

Modification of lignin by Geotrichum klebahnii

¹³C-NMR spectroscopic analysis indicates that the yeast-like species Geotrichum klebahnii is an efficient microorganism for lignin biodegradation. This strain modified beechwood lignin even if it was the only carbon source by C-C side chain cleavage, C-oxidations, aromatic ring cleavage and reductive reactions. The obtained results outline prospective application of G. klebahnii for biotechnological pre-treatment of lignocellulosic materials.     

Chemolithoutotrophic growth of Thiothrix ramosa

Thiothrix has been shown for the first time to be able to grow chemolithoautotrophically with thiosulphate or carbon disulphide as sole energy substrate. Thiosulphate served as the growth-limiting substrate for Thiothrix ramosa in chemostat culture. Maximum growth yield (Y_max) from yields at growth rates between 0.029–0.075 h^-1 was 4.0 g protein/mol thiosulphate oxidized. The key enzyme of the Calvin cycle, ribulose 1,5-bisphosphate carboxylase, was present in these cells, as were rhodanese, adenylyl sulphate (APS) reductase and sulphur-oxidizing enzyme. Thiosulphate-grown cells oxidized thiosulphate, sulphide, tetrathionate and carbon disulphide. Oxidation kinetics for sulphide, thiosulphate and tetrathionate were biphasic: oxygen consumption during the fast first phase of oxidation indicated oxidation of sulphide, and the sulphane moieties of thiosulphate and tetrathionate, to elemental sulphur, before further oxidation to sulphate. Kinetic constants for these four substrates were determined. T. ramosa also grew mixotrophically in batch culture on lactate with a number of organic sulphur compounds: carbon disulphide, methanethiol and diethyl sulphide. Substituted thiophenes were also used as sole substrates. The metabolic versatility of T. ramosa is thus much greater than previously realised.     

Chemolithotrophic potential of a Hyphomicrobium species,capable of growth on methylated sulphur compounds

The yield of Hyphomicrobium EG on dimethyl sulphoxide, dimethyl sulphide and methylamine, considering the metabolic pathways of these compounds, suggested that the organism gained energy from the oxidation of the sulphur moiety of the former compounds. Indeed, a comparison of chemostat cultures of Hyphomicrobium EG grown on methylamine in the presence and absence of sulphide or thiosulphate proved this obligate methylotroph to be a chemolithoheterotroph. The apparent Y_sulphide and Y_thiosulphate were comparable, being 8–10 g dry weight/mol. In batch cultures thiosulphate concentrations up to 10 mM had a stimulatory effect on the growth rate of Hyphomicrobium EG, whereas higher concentrations increased the organisms doubling time.Enzyme- and respiration data showed that the organism had constitutive enzymes for the breakdown of dimethyl sulphoxide although they were clearly regulated to need. Addition of sulphide or thiosulphate to methylamine-limited chemostat cultures of Hyphomicrobium EG not only resulted in the induction of enzymes necessary for their breakdown, but also caused the enzymes for dimethyl sulphoxide metabolism, especially methyl mercaptan oxidase, to be induced. The formation of H₂O₂, a product of the latter enzyme, was reflected in the relatively high catalase activities during growth on dimethyl sulphoxide and in the organisms inability to grow on this compound in the presence of a catalase inhibitor.Abbreviations DMSO dimethyl sulphoxide - DMS dimethyl sulphide - MM methyl mercaptan - TMAO trimethylamine N-oxide - D dilution rate - GSH redticed glutathione - DCPIP 2,6-dichlorophenolindophenol - PMS phenazine methosulphate - PES phenazine ethosulphate - RubPCase ribulose 1,5-bisphosphate carboxylase - PEPCase phosphoenol pyruvate carboxylase - Wurster's blue (TMPD) N,N,N,N-tetramethyl-p-phenylenediamine     

Partial purification and properties of guanosine triphosphate cyclohydrolase from Drosophila melanogaster

The first enzyme (named GTP cyclohydrolase) in the pathway for the biosynthesis of pteridines has been partially purified from extracts of late pupae and young adults of Drosophila melanogaster. This enzyme catalyzes the hydrolytic removal from GTP of carbon 8 as formate and the synthesis of 2-amino-4-hydroxy-6-(d-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine triphosphate (dihydroneopterin triphosphate). Some of the properties of the enzyme are as follows: it functions optimally at pH 7.8 and at 42 C; activity is unaffected by KCl and NaCl, but divalent cations (Mg²⁺, Mn²⁺, Zn²⁺, and Ca²⁺) are inhibitory; the K _m for GTP is 22 m; and the molecular weight is estimated at 345,000 from gel filtration experiments. Of a number of nucleotides tested, only GDP and dGTP were used to any extent as substrate in place of GTP, and these respective compounds were used only 1.8% and 1.5% as well as GTP.This work was supported by research grants from the National Institutes of Health (AM03442) and the National Science Foundation (GB33929).     

Sulfide oxidation in Ectothiorhodospira abdelmalekii. Evidence for the catalytic role of cytochrome c-551

A cytochrome c-551 was isolated and purified from Ectothiorhodospira abdelmalekii. It is a small acidic haemoprotein with a molecular weight of 9,500, an isoelectric point of 3.5 and a redox potential of-7 mV at pH 7.0. It showed three maxima in the reduced state (=551, =529, =417). The best purity index (A₂₈₀/A₄₁₇) obtained was 0.29. During sulfide oxidation to elemental sulfur a considerable amount of polysulfides were transiently accumulated. The digestion experiment can be taken to indicate that cytochrome c-551 is localized on the outside of the cell membrane. The addition of cytochrome c-551 to a suspension of spheroplasts stimulated the velocity of sulfide oxidation. These experiments support the interpretation that cytochrome c-551 may be a sulfide: acceptor oxidoreductase.In memory of Prof. Yousef Abd-el-Malek, who died in a traffic accident February 12, 1983     

Age-related effects in enzyme catalysis

Summary Rat muscle glyceraldehyde-3-phosphate dehydrogenase is one of several enzymes which have been found to undergo age-related modifications. While the amount of this enzyme in muscle tissue does not change with age, both its specific activity and affinity towards its co-enzyme are significantly reduced in the old tissue.Age-related structural changes were found to exist in the nicotinamide binding site of the enzyme and the reactions leading to the activity loss in old glyceraldehyde-3-phosphate dehydrogenase were shown to involve a reversible modification of the essential cysteine-149 residue at the active site of the enzyme. The aging effects were simulated by a controlled oxidation of cys-149 in samples of young glyceraldehyde-3-phosphate dehydrogenase and subsequent reduction of this residue by 2-mercaptoethanol. The enzyme modified in this way closely resembles native old glyceraldehyde-3-phosphate dehydrogenase, indicating that the structural modifications in the latter enzyme are indeed introduced by a post-translational process. The mechanism for aging of glyceraldehyde-3-phosphate dehydrogenase which is proposed, based on these observations, thus assumes an oxidation of cys-149 as its first step followed by irreversible conformational changes in the enzyme molecule. The aging of glyceraldehyde-3-phosphate dehydrogenase may thus be triggered by the reduced ability of old muscle tissue to protect its constituents against oxidation.Abbreviations CPL circular polarization of luminescence - DTNB 5,5-dithiobis (2-nitrobenzoic acid) - GPDH D-glyceraldehyde-3-phosphate dehydrogenase - ENAD⁺ nicotinamide 1,N⁶-ethenoadenine dinucleotide     

Isolation and characterization of oil-desulphurizing bacteria

The objective of this study was to isolate local bacterial strains capable of removing sulphur from oil fractions without degrading the hydrocarbon. Oil biodesulphurization is an important step in combating pollution problems emanating from burning fossil fuels. Organisms which survive on oil are plentiful in local Kuwaiti soils; however, those that selectively only attack the carbon–sulphur bond are more difficult to find. Three strains were isolated based on their ability to use dibenzothiophene (DBT) as a sole source of sulphur for growth at 30 °C. Similar to other biodesulphurization organisms, the strains convert DBT to [2-hydroxybiphenyl (2-HBP) as detected by gas chromatography (GC). The specific desulphurization activity was in the range 5–13 mol 2-HBP/g-cell × h. Identification of the strains, based on 16 rRNA gene sequence similarity, showed the strains to be Rhodococcus erythropolis and Rhodococcus globerulus. The biodesulphurization activity was enhanced by promoting oxidore-ductase enzyme co-expression through the addition of a carbon source. The desulphurization was limited by the availability of DBT to the organism. Interfacial mass transfer through the aqueous-organic layer was confirmed to be a limiting factor.     

Influence of inorganic microelements on the production of camptothecin with suspension cultures of <Emphasis Type="Italic">Camptotheca acuminata</Emphasis>

The effects of eight microelements (I^–, BO₃ ^3–, MoO₄ ^2–, Co²⁺, Cu²⁺, Mn²⁺, Fe²⁺, Zn²⁺) on the biosynthesis of camptothecin and the growth of suspension cultures of Camptotheca acuminata were studied. The increase of I^– to 25 M l^–1, Cu²⁺ to 1 M l^–1, Co²⁺ to 2 M l^–1 and MoO₄ ^2– to 10 M l^–1 in Murashige and Skoog (MS) medium resulted in 1.66, 2.84, 2.53 and 2.04 times higher of camptothecin yield than that in standard MS medium respectively. Combined treatment of I^– (25 M l^–1), Cu²⁺ (1 M l^–1), Co²⁺ (2 M l^–1) and MoO₄ ^2– (10 M l^–1) lead to improve cell dry weight, camptothecin content, and camptothecin yield to 30.56 g l^–1, 0.0299%, and 9.15 mg l^–1, respectively, which were 20.2, 208.9 and 273.8% increment respectively when compared with those of control.