不同pH值条件下硫酸盐还原菌组成及硫酸盐还原机制分析

【目的】从海洋沉积物中富集获得硫酸盐还原菌群,改变pH值进行培养,分析pH值对硫酸盐还原性质的影响,明确菌群组成和进行硫酸盐还原功能基因预测,探究硫酸盐还原机制。【方法】分析硫酸盐还原菌群在不同pH值条件下的硫酸盐还原率,在此基础上,利用高通量测序技术和PICRUSt软件分析硫酸盐还原菌群优势菌组成及硫酸盐还原相关基因相对丰度。【结果】硫酸盐还原菌群在不同pH值培养条件下的生长和硫酸盐还原率出现显著变化(P<0.01),在pH 5.0时达到峰值,分别为0.34±0.01和96.52%±0.44%。高通量测序数据显示,pH 5.0时菌群丰富度和多样性最高,优势菌属为假单胞菌(Pseudomonas)和芽孢杆菌(Bacillus),相对丰度较高的基因为同化性硫酸盐还原相关基因。【结论】硫酸盐还原菌富集生长的最适pH 5.0,在此条件下的高硫酸盐还原率由同化性硫酸盐还原途径主导,为揭示硫酸盐还原机制提供了实验支持,并拓宽了硫酸盐还原菌实践应用方面的种质资源。     

Enhanced dissolution of silicate minerals by bacteria at near-neutral pH

Previous studies have shown that various microorganisms can enhance the dissolution of silicate minerals at low (<5) or high (>8) pH. However, it was not known if they can have an effect at near-neutral pH. Almost half of 17 isolates examined in this study stimulated bytownite dissolution at near-neutral pH while in a resting state in buffered glucose. Most of the isolates found to stimulate dissolution also oxidized glucose to gluconic acid. More detailed analysis with one of these isolates suggested that this partial oxidation was the predominant, if not sole, mechanism of enhanced dissolution. Enhanced dissolution did not require direct contact between the dissolving mineral and the bacteria. Gluconate-promoted dissolution was also observed with other silicate minerals such as albite, quartz, and kaolinite.Correspondence to: D.L. Kirchman.     

Colony formation of free-living and particle-associated sulfate-reducing bacteria

Abstract Some of the components that are likely to be involved in the respiratory chains that transfer electrons from the ferrous iron substrate of various acidophilic bacteria have been revealed by spectroscopic analysis. An apparently unique, soluble and acid-stable cytochrome was found in Leptospirillum ferrooxidans which appeared to lack any of the major cytochromes or the rusticyanin of the better-studied iron-oxidizing mesophile, Thiobacillus ferrooxidans . A specific absorption peak, only found in iron-grown cells, was revealed in a whole cell spectra of thermoacidophilic archaebacteria of different genera.     

Interactions between acidic matrix macromolecules and calcium phosphate ester crystals: relevance to carbonate apatite formation in biomineralization.

Control over crystal growth by acidic matrix macromolecules is an important process in the formation of many mineralized tissues. Earlier studies on the interactions between acidic macromolecules and carboxylate- and carbonate-containing crystals showed that the proteins recognize a specific stereochemical motif on the interacting plane. Here we show that a similar stereochemical motif is recognized by acidic mollusc shell macromolecules interacting with four different organic calcium phosphate-containing crystals. In addition, an acidic protein from vertebrate tooth dentin was also observed to recognize a similar structural motif in one of the crystals. The characteristic motif recognized is composed of rows of calcium ions and phosphates arranged in a plane defined by two free oxygens and a phosphorus atom emerging perpendicular to the affected face. These observations may have a direct bearing on the manner in which control over crystal growth is exerted on carbonate apatite crystals commonly found in vertebrate tissues.     

New sulfate-reducing bacteria isolated from Buryatian alkaline brackish lakes: description of Desulfonatronum buryatense sp. nov

New strains of sulfate-reducing bacteria were isolated from two alkaline brackish lakes located in the Siberian region of Russia, namely in the Southern Transbaikalia, Buriatia. The article presents data describing morphology, physiology, and biochemical characteristics of the isolated strains. These strains Ki4, Ki5, and Su2 were mesophilic and alkaliphilic with optimal growth at pH 8.9, 9.4, and 10.0, respectively. All isolated strains utilized lactate, formate, and ethanol in the presence of sulfate for growth and sulfidogenesis accompanied with formation of acetate and CO₂. Strains Ki5 and Su2 were able to reduce Fe(III). The DNA G + C content in strains Ki4, Ki5 and Su2 was 56.3, 48.8 and 59.6 mol%, respectively. According to phylogenetic analysis of 16S rRNA sequences, the new strains were clustered within the genus Desulfonatronum, and the closest relative D. lacustre Z-7951^T (=DSM 10312^T) showed 99.3–99.6 % similarity. DNA–DNA relatedness values of the strains Ki4, Ki5, and Su2 with D. lacustre Z-7951^T were 89, 53, and 79 %, respectively. Polyphasic taxonomy data suggest that strain Ki5^T is representative of the proposed novel species Desulfonatronum buryatense sp. nov.     

The effect of sodium salts and pH on hydrogenase activity of the haloalkaliphilic sulfate-reducing bacteria

Hydrogenase is the main catabolic enzyme of hydrogen-utilizing sulfate-reducing bacteria. In haloalkaliphilic sulfate reducers, hydrogenase, particularly if it is periplasmic, functions at high concentrations of Na+ ions and low concentrations of H+ ions. The hydrogenases of the newly isolated sulfate-reducing bacteria Desulfonatronum thiodismutans, D. lacustre, and Desulfonatrovibrio hydrogenovorans exhibit different sensitivity to Na+ ions and remain active at NaCl concentrations between 0 and 4.3 M and NaHCO3 concentrations between 0 and 1.2 M. The hydrogenases of D. lacustre and D. thiodismutans remain active at pH values between 6 and 12. The optimum pH for the hydrogenase of D. thiodismutans is 9.5. The optimum pH for the cytoplasmic and periplasmic hydrogenases of D. lacustre is 10. Thus, the hydrogenases of D. thiodismutans, D. lacustre, and Dv. hydrogenovorans are tolerant to high concentrations of sodium salts and extremely tolerant to high pH values, which makes them unique objects for biochemical studies and biotechnological applications.     

Growth of methanogenic and sulfate-reducing bacteria with cathodic hydrogen

Summary Bacteria contribute to corrosion in various ways. Therefore the consumption of cathodic hydrogen as well as the sulfide production of sulfate-reducing bacteria may influence the anaerobic corrosion of iron. Also methanogenic bacteria are able to use elemental iron as a source of electrons for carbon dioxide reduction. We have studied both processes and have got evidence that cathodic depolarisation does not play a dominant role in methanogenic habitats.     

Enrichment of sulfate-reducing bacteria and resulting mineral formation in media mimicking pore water metal ion concentrations and pH conditions of acidic pit lakes

Acid mine drainage sites are extreme environments with high acidity and metal ion concentrations. Under anoxic conditions, microbial sulfate reduction may trigger the formation of secondary minerals as a result of H2S production and pH increase. This process was studied in batch experiments with enrichment cultures from acidic sediments of a pit lake using growth media set at different pH values and containing elevated concentrations of Fe2? and Al3?. At initial pH values of 5 and 6, sulfate reduction occurred shortly after inoculation. Sulfate- reducing bacteria affiliated to the genus Desulfosporosinus predominated the microbial communities as shown by 16S rRNA gene analysis performed at the end of the incubation. At initial pH values of 3 and 4, sulfate reduction and cell growth occurred only after an extended lag phase, however, at a higher rate than in the less acidic assays. At the end of the growth phase, enrichments were dominated by Thermodesulfobium spp. suggesting that these sulfate reducers were better adapted to acidic conditions. Iron sulfides in the bulk phase were common in all assays, but specific aluminum precipitates formed in close association with cell surfaces and may function as a detoxification mechanism of dissolved Al species at low pH.     

Key roles of pH and calcium metabolism in microbial carbonate precipitation

This paper reviews the general mechanismsof microbial carbonate precipitation and offersan alternative view on the role of calciummetabolism in this process, as well as on theoccurrence of species- and environment-specificcalcification.     

Characterization of hyaluronic acid interaction with calcium oxalate crystals: implication of crystals faces, pH and citrate

Interaction between hyaluronic acid (HA) present at the surface of tubular epithelial cells and calcium oxalate monohydrate (COM) crystals is thought to play an important role in kidney stone formation. AFM-based force spectroscopy, where HA is covalently attached to AFM-probes, was used to quantify the interaction between HA and the surfaces of COM crystals. The work of adhesion of the HA-probe as well as the rupture force of single HA molecules were quantified in order to understand the molecular regulation of HA binding to COM crystals. Our results reveal that HA adsorbs to the crystal surface in physiological conditions. We also observed increased adhesion when the pH is lowered to a value that increases the risk of kidney stone formation. HA adhesion to the COM crystal surface can be suppressed by citrate, a physiological inhibitor of stone retention currently used in the treatment and prevention of kidney stone formation. Interestingly, we also observed preferential binding of HA onto the [100] face versus the [010] face, suggesting a major contribution of the [100] faces in the crystal retention process at the surface of tubular epithelial cells and the promotion of stone formation. Our results clearly establish a direct role for the glycosaminoglycan HA present at the surface of kidney tubular epithelium in the process of COM crystal retention.     

Schistosoma mansoni: eggshell formation is regulated by pH and calcium

The protein precursors of the schistosome eggshell are synthesized and packaged into secretory vesicles in the vitelline cells. These vesicles appear to contain an emulsion of eggshell precursor material. Evidence is presented to show that these secretory vesicles are acidic as in other systems and that this acidity stabilizes the emulsion and prevents the eggshell cross-linking reactions from occurring. Alkalinizing treatments trigger eggshell formation within the secretory vesicles as shown by (1) the induction of autofluorescence and (2) by electron microscopy which shows that the eggshell precursors have aggregated within the secretory vesicles into spherical particles bearing microspines. These aggregates formed in the secretory vesicles were isolated and shown to have the same protease resistance and amino acid composition as authentic eggshell. The calcium ionophore A23187 induces scattered autofluorescence in intact female worms which electron micrographs show to be due to exocytosis of eggshell material. Based on these observations we propose a model for the formation of schistosome eggshell and suggest that it may apply to all trematodes in which the eggshell precursors are present as stable emulsions in the secretory vesicles of the vitelline cells.     

Mollusc larval shell formation: amorphous calcium carbonate is a precursor phase for aragonite

The larval shells of the marine bivalves Mercenaria mercenaria and Crassostrea gigas are investigated by polarized light microscopy, infrared spectroscopy, Raman imaging spectroscopy, and scanning electron microscopy. Both species contain similar shell ultrastructures. We show that larval shells contain amorphous calcium carbonate (ACC), in addition to aragonite. The aragonite is much less crystalline than non-biogenic aragonite. We further show that the initially deposited mineral phase is predominantly ACC that subsequently partially transforms into aragonite. The postset juvenile shell, as well as the adult shell of Mercenaria also contains aragonite that is less crystalline than non-biogenic aragonite. We conclude that ACC fulfills an important function in mollusc larval shell formation. It is conceivable that ACC may also be involved in adult shell formation.     

In macropore tryptic digestion at acidic pH and its implication for proteomics

Gan et al. (Proteomics 2013, 13, 3117–3123) described a new “macropore” protocol for effective protein digestion by trypsin suitable for a wide range of pH including acidic pH. It was effective not only in experiments with solutions of a model protein (myoglobin), but also with a subfraction of rat liver cytosol. This significantly simplifies and accelerates protein digestion procedures for subsequent MS. However, further studies are needed to find limits of experimental applicability of the described protocol in proteomics.     

Polyacrylamide gel electrophoresis: reaction of acrylamide at alkaline pH with buffer components and proteins

The chemical reaction of monomeric acrylamide with primary, secondary, and tertiary amines, used as buffer components in polyacrylamide gel electrophoresis systems, was investigated in the basic pH range. Adduct formation proceeded for several minutes up to weeks, depending on the reactivity of the amino groups. A pH shift in the reaction mixture due to an altered pK value of the reaction product was observed. However, a few primary amines (tris(hydroxymethyl)aminomethane, 2-amino-2-methyl-1,3-propanediol) and secondary amines 3-([2-hydroxy-1,1-bis(hydroxymethyl)ethyl]amino)-1-propanesulfonic acid, 3-(dimethyl(hydroxymethyl)methylamino)-2-hydroxypropanesulfonic acid) showed negligible shifts of pH. They are, therefore, useful as components in the polymerization mixture; whereas some tertiary amines showing complete pH stability as well (e.g., triethanolamine) are not suitable, as they acted as accelerators of gel polymerization. Acrylamide can also covalently bind to proteins by reacting with the epsilon-amino group of lysine residues, especially. Bovine serum albumin, having an acidic isoelectric point, and the basic protein cytochrome c were treated with different acrylamide concentrations at alkaline pH yielding modified protein molecules with altered electrophoretic mobilities in different polyacrylamide gel electrophoresis systems. This reaction gave rise to artifacts in alkaline polyacrylamide gels and isoelectric focusing systems when residual acrylamide monomers were still present in the gel matrix after the polymerization process ceased.     

Conformational states of beta-lactamase: molten-globule states at acidic and alkaline pH with high salt

We present evidence that beta-lactamase is close to fully unfolded (i.e., random coil conformation) at low ionic strength at the extremes of pH and that the presence of salt causes a cooperative transition to a conformation with the properties of a molten globule, namely, a compact state with native-like secondary structure but disordered side chains (tertiary structure). The conformation of beta-lactamase I from Bacillus cereus was examined over the pH 1.5-12.5 region by circular dichroism (CD), tryptophan fluorescence, dynamic light scattering, and 1-anilino-8-naphthalenesulfonate (ANS) binding. Under conditions of low ionic strength (I = 0.05) beta-lactamase was unfolded below pH 2.5 and above pH 11.5, on the basis of the far-UV and near-UV CD and tryptophan fluorescence. However, at high ionic strength and low pH an intermediate conformation (state A) was observed, with a secondary structure content similar to that of the native protein but a largely disordered tertiary structure. The transition from the unfolded state (U) to state A induced by KCl was cooperative and had a midpoint at 0.12 M KCl (I = 0.17 M) at pH 1.6. A similar conformation (state B) was observed at high pH and high ionic strength. The transition from the alkaline U state to state B induced by KCl at pH 12.2 was cooperative and had a midpoint at 0.6 M KCl (I = 0.65 M). Light scattering measurements showed that state B was compact although somewhat expanded compared to the N state. The compactness of state A could not be determined due to its strong propensity to aggregate.(ABSTRACT TRUNCATED AT 250 WORDS)     

硫酸盐还原细菌生物被膜的形成与调控研究进展

硫酸盐还原细菌(sulfate-reducing bacteria,SRB)形成的生物被膜是微生物导致金属锈蚀行为的主要原因,同时也是重金属污水微生物修复技术的关键因子。生物被膜形成及调控机制研究对SRB的防治和利用均十分重要。本文综述了近年来SRB生物被膜的研究进展,包括SRB生物被膜的胞外多聚物组成和控制因子,并着重阐述了目前已知的调控因子对SRB生物被膜形成的影响。     

Glycine-assisted enhancement of 1,4-beta-d-xylan xylanohydrolase activity at alkaline pH with a pH optimum shift

This is the first report describing the enhancement of xylanase activity by the neutral amino acid glycine. Xylanase activity is increased seven-fold at alkaline pH in the presence of glycine and its pH optimum is shifted from pH 7 to 8 without using any protein engineering techniques. Analysis of the steady-state kinetics revealed that glycine in the reaction mixture increases the K(m) and k(cat) values of the enzyme. Chemoaffinity labeling and studies using glycine esters indicate an involvement of the carboxylate ion of glycine in enhancing xylanase catalytic activity. A novel possible mechanism for the glycine-assisted catalytic action of xylanase is proposed.     

The pH dependence of proton-deuterium exchange, hydrogen production and uptake catalyzed by hydrogenases from sulfate-reducing bacteria

Different patterns have been found in the pH dependence of hydrogenase activity with enzymes purified from different species of Desulfovibrio. With the cytoplasmic hydrogenase from Desulfovibrio baculatus strain 9974, the pH optima in H2 production and uptake were respectively 4.0 and 7.5 with a higher activity in production than in uptake. The highest D2-H+ exchange activity was found also at pH 4.0 but the optima differed for the HD and the H2 components. Both similarly rose when the pH decreased from 9.0 to 4.5, but the rate of H2 evolution slowed whereas the HD evolution continued rising till pH values around 3.0 were reached. The H2 to HD ratio at pH above 4.5 was higher than one. With the periplasmic hydrogenase from Desulfovibrio vulgaris Hildenborough, the highest exchange activity was near pH 5.5, the same value as in hydrogen production. The periplasmic hydrogenase from Desulfovibrio gigas had in contrast the same pH optimum in the exchange (7.5-8.0) as in the H2 uptake. The ratio of H2 to HD was below one for both enzymes. These different patterns may be related to functional and structural differences in the three hydrogenases so far studied, particularly in the composition of their catalytic centers.