Enzymatic profiles of 11 barophilic bacteria under in situ conditions: evidence for pressure modulation of phenotype.

Barophilic bacteria are microorganisms that grow preferentially (facultative barophiles) or exclusively (obligate barophiles) under elevated hydrostatic pressure. Barophilic bacteria have been isolated from a variety of deep-sea environments. Attempts to characterize these organisms have been hampered by a lack of appropriate methodologies. A colorimetric method for the detection of 19 constitutively expressed enzymes under in situ conditions of pressure and temperature has been devised, using a simple modification of the commercially available API ZYME enzyme assay kit. By using this method, enzyme profiles of 11 barophilic isolates, including an obligate barophile, were determined. Nine of the 10 facultatively barophilic isolates examined exhibited a change of phenotype in at least one enzyme reaction when tested at 1 atm (1 atm = 101.29 kPa), compared with results obtained under in situ pressure. The assay is simple and rapid and allows for direct determination of enzyme activity under conditions of high pressure and low temperature.     

Enzymatic adaptation by bacteria under pressure.

A study of enzymic adaptation under hydrostatic pressure by moderately barotolerant bacteria that can grow at pressure up to about 500 atm revealed that some adaptive processes are relatively insensitive to pressure, whereas others are sufficiently barosensitive to compromise survival capacity in situations requiring adaptation to new substrates under pressure. Examples of the former include adaptation of Escherichia coli to arabinose catabolism for growth and adaptation of Streptococcus faecalis to catabolism of lactose, ribose, or maltose. Examples of the latter include derepression of the lac operon in Escherichia coli and induction of penicillinase synthesis by Bacillus licheniformis. For both these barosensitive systems, pressure had little effect on enzyme levels in constitutive strains or in bacteria that had previously been induced at 1 atm. Moreover, it had no detectable effect on penicillinase secretion. However, pressures of 300 to 400 atm were found to reduce markedly rates and extents of enzyme synthesis by bacteria undergoing derepression or adaptation. This inhibitory effect of pressure was reflected in greater barosensitivity with extended lag and slower growth of initially unadapted Escherichia coli cells inoculated into minimal medium with lactose as sole source of carbon and fuel, and by major reductions in the minimal inhibitory concentrations of penicillin G for unadapted B. licheniformis cells inoculated into complex, antibiotic-containing media. Cyclic adenosine 5'-monophosphate did not reverse pressure inhibition of derepression of the lac operon, and catabolite repression was complete under pressure. However, derepression of the lac operon was more sensitive to pressure at low concentrations of inducer than at high concentrations. Apparent volume changes for derepression were 94 and 60 ml/mol at inducer concentrations of about 0.5 and 5 mM, respectively. Pressure was found not to be inhibitory for uptake of beta-galactosides; in fact, it was somewhat stimulatory. Therefore, results were interpreted in terms of inducer binding and subsequent conversion of an operator-inducer-repressor complex to inactive repressor and operator. Both reactions appeared to result in an increase in volume, the former more so than the latter. We found also that 200 atm was actually stimulatory for growth of Escherichia coli in minimal media, and the bacterium was in a sense barophilic.     

Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization

A technique based on quantitative microautoradiography (QMAR) and fluorescence in situ hybridization (FISH) was developed and evaluated in order to determine the quantitative uptake of specific substrates in probe-defined filamentous bacteria directly in a complex system. The technique, QMAR-FISH, has a resolution of a single cell and is based on an improved fixation protocol and the use of an internal standard of bacteria with known specific radioactivity. The method was used to study the in situ ecophysiology of the filamentous bacteria 'Candidatus Meganema perideroedes' and Thiothrix sp. directly in an activated sludge system. The cellular uptake rate of tritium-labelled substrates revealed an average cell-specific uptake rate of 4.1 yen 10-15 mol of acetate cell-1 h-1 and 3.1 yen 10-15 mol of acetate cell-1 h-1 for the two filamentous species respectively. The two filamentous species had very similar activity in all cells along each filament. Surprisingly, the filaments within both probe-defined populations had threefold variation in activity between the different filaments, demonstrating a large variation in activity level within a single population in a complex system. The substrate affinity (Ks) for uptake of acetate of the cells within the two filamentous bacteria was determined by incubation with variable concentrations of labelled acetate. The Ks values of the 'Candidatus Meganema perideroedes' and the Thiothrix filamentous bacteria were determined to be 1.8 micro M and 2.4 micro M acetate respectively.     

Integration of bacteria capture via filtration and in situ lysis for recovery of plasmid DNA under industry-compatible conditions

Combining capture and lysis of the bacteria with partial purification of the plasmid DNA is beneficial for the design of efficient plasmid production processes at larger scale. Such an approach is possible when the bacteria are captured by filtration. Taking industrial requirements into account, however, such a capture requires complex filtration mixtures containing retentive additives such as bentonite and polycations. This makes the straightforward transfer of established lysis protocols to in situ lysis difficult. In this contribution, the different steps of such a protocol are designed for complex filter cakes, including fragilization (by lysozyme), lysis (alkaline pH/acidic pH, 70/37 degrees C, urea/NaCl/Triton), and specific elution (pH, NaCl, CaCl2, guanidinium hydrochloride). Results are compared in regard to plasmid quality (topoisomeric form) and quantity (compared to the yield obtained by a commercial miniprep of a small aliquot of the bacteria suspension from the bioreactor). Best results in these terms were obtained by the Triton lysis protocol performed at 37 degrees C (30 min of contact with a lysis buffer composed of 50 mM Tris pH 8, 1% Triton, 1 g/L lysozyme, and 6 M guanidinium hydrochloride) followed by the specific elution of the plasmid DNA in 50 mM Tris buffer pH 8.     

不同压力条件下油藏内源细菌群落激活过程中变性梯度凝胶电泳分析?

摘要：【目的】了解常压（1 MPa）和高压（10 MPa）条件下内源细菌激活中的细菌群落和结构的变化。【方法】利用胜利油田沾3×24井产出液水样,在常压和高压下进行富集培养后,定时取样,样品用变性梯度凝胶电泳（denature gradient gel electrophoresis,DGGE）技术分析。【结果】通过对内源微生物激活前后DGGE条带的数量和亮度变化分析表明,油藏环境中的细菌在种类和数量上并不丰富,激活剂的加入改变了菌群原有的贫营养环境,从而使一些因营养缺乏生长受抑制细菌得以大量繁殖,菌群结     

A stress protein is induced in the deep-sea barophilic hyperthermophile Thermococcus barophilus when grown under atmospheric pressure

The whole-cell protein inventory of the deep-sea barophilic hyperthermophile Thermococcus barophilus was examined by one-dimensional SDS gradient gel electrophoresis when grown under different pressure conditions at 85°C (T _opt). One protein (P60) with a molecular mass of approximately 60 kDa was prominent at low pressures (0.3 MPa hydrostatic pressure and 0.1 MPa atmospheric pressure) but not at deep-sea pressures (10, 30, and 40 MPa). About 17 amino acids were sequenced from the N-terminal end of the protein. Sequence homology analysis in the GenBank database showed that P60 most closely resembled heat-shock proteins in some sulfur-metabolizing Archaea. A high degree of amino acid identity (81%–93%) to thermosome subunits in Thermococcales strains was found. Another protein (P35) with molecular mass of approximately 35.5 kDa was induced at 40 MPa hydrostatic pressure but not under low-pressure conditions. No amino acid sequence homology was found for this protein when the 40 amino acids from the N-terminal end were compared with homologous regions of proteins from databases. A PTk diagram was generated for T. barophilus. The results suggest that P _habitat is about 35 MPa, which corresponds to the in situ pressure where the strain was obtained. Received: May 14, 1999 / Accepted: July 30, 1999     

Benzene oxidation under sulfate-reducing conditions in columns simulating in situ conditions

The oxidation of benzene under sulfate-reducing conditions was examined in column and batch experiments under close to in situ conditions. Mass balances and degradation rates for benzene oxidation were determined in four sand and four lava granules filled columns percolated with groundwater from an anoxic benzene-contaminated aquifer. The stoichiometry of oxidized benzene, produced hydrogen carbonate and reduced sulfate correlated well with the theoretical equation for mineralization of benzene with sulfate as electron acceptor. Mean retention times of water in four columns were determined using radon (²²²Rn) as tracer. The retention times were used to calculate average benzene oxidation rates of 8–36 μM benzene day⁻¹. Benzene-degrading, sulfide-producing microcosms were successfully established from sand material of all sand filled columns, strongly indicating that the columns were colonized by anoxic benzene-degrading microorganisms. In general, these data indicate a high potential for Natural Attenuation of benzene under sulfate-reducing conditions at the field site Zeitz. In spite of this existing potential to degrade benzene with sulfate as electron acceptor, the benzene plume at the field site is much longer than expected if benzene would be degraded at the rates observed in the column experiment, indicating that benzene oxidation under sulfate-reducing conditions is limited in situ.     

Expression profiles of sugarcane under drought conditions: Variation in gene regulation

Drought is a major factor in decreased sugarcane productivity because of the resulting morphophysiological effects that it causes. Gene expression studies that have examined the influence of water stress in sugarcane have yielded divergent results, indicating the absence of a fixed pattern of changes in gene expression. In this work, we investigated the expression profiles of 12 genes in the leaves of a drought-tolerant genotype (RB72910) of sugarcane and compared the results with those of other studies. The genotype was subjected to 80–100% water availability (control condition) and 0–20% water availability (simulated drought). To analyze the physiological status, the SPAD index, Fv/Fm ratio, net photosynthesis (A), stomatal conductance (g _s) and stomatal transpiration (E) were measured. Total RNA was extracted from leaves and the expression of SAMDC, ZmPIP2-1 protein, ZmTIP4-2 protein, WIP protein, LTP protein, histone H3, DNAj, ferredoxin I, β-tubulin, photosystem I, gene 1 and gene 2 was analyzed by quantitative real-time PCR (RT-PCR). Important differences in the expression profiles of these genes were observed when compared with other genotypes, suggesting that complex defense mechanisms are activated in response to water stress. However, there was no recognizable pattern for the changes in expression of the different proteins associated with tolerance to drought stress.     

An in situ dissolved-hydrogen probe for monitoring anaerobic digesters under overload conditions

The concentration of diatomic hydrogen in the liquid phase of an anaerobic digester was used to determine the onset of digester failure induced by substrate overloading. The construction of an inexpensive probe to measure dissolved hydrogen, having a partial pressure detection limit of 30 Pa, is described. An increase in the partial pressure of dissolved hydrogen, from less than 30 Pa to 400 Pa, was observed when the D-glucose concentration in a laboratory-scaled digester was increased rapidly to 10 mM. However, when the digester was gradually overloaded, an increase in the dissolved-hydrogen partial pressure was not observed until after the digester failed. The accumulation of volatile fatty acids and digester failure were observed at dissolved-hydrogen partial pressures below 30 Pa. (c) 1995 John Wiley & Sons, Inc.     

Sexual conflict and polyspermy under sperm-limited conditions: in situ evidence from field simulations with the free-spawning marine echinoid Evechinus chloroticus

For free-spawning organisms that release gametes into the sea, sperm limitation (too few sperm to fertilize all eggs) is a major factor limiting reproductive success. Given such circumstances, the presence of several mechanisms to prevent polyspermy (too many sperm) may seem paradoxical; however, a growing body of data suggests that natural fertilization levels, though variable, can routinely be high. Under such conditions, polyspermy is much more likely. The tension between sperm limitation and polyspermy represents sexual conflict because males, in competing to fertilize as many eggs as possible, can impose lethal costs on eggs if multiple sperm gain entry. Here we present data for a marine invertebrate indicating high levels of polyspermy under sperm-limited conditions. When the sea urchin Evechinus chloroticus was induced to spawn in situ, mean rates of polyspermy were [Formula: see text], and polyspermy was recorded at rates as high as 62.7%. Polyspermy was nearly always present, even when fertilization rates were <50%, confirming predictions that it should be present under sperm-limited conditions. Both sperm limitation and polyspermy imposed substantial reproductive costs, and we conclude that both sexual conflict related to polyspermy and sperm limitation have been simultaneous strong selective forces shaping the evolution of reproductive traits in the sea.     

Enzymatic hydrolysis of cellulose: Evaluation of cellulase culture filtrates under use conditions

Culture filtrates from three mutant strains of Trichoderma reesei grown on lactose and on cellulose were compared under use conditions on four cellulose substrates. Cellulose culture filtrates contained five to six times as much cellulase as lactose culture filtrates. Unconcentrated cellulose culture filtrates produced up to 10% sugar solutions from 15% cellulose in 24 h. Specific activity in enzyme assays and efficiency in saccharification tests were low for enzymes from all the mutants. Over a wide range the percent saccharification of a substrate in a given times was directly proportional to the logarithm of the ratio of initial concentrations of enzyme and substrate. As a result of this, dilute enzyme is more efficient than concentrated enzyme, but if high sugar concentrations are desired, very large quantities of enzyme are required. Since the slopes of these plots varied, the relative activity of cellulase on different substrates may be affected by enzyme concentration.     

Batch culture of bacteria under controlled gaseous conditions

Summary A flask, designed for direct gassing of batch cultures of bacteria, was evaluated for its use in studying oxygen absorption rates (OAR) and suitability for physiological studies under various controlled atmospheres. Such flasks, aerated directly without shaking, yielded an OAR (up to 1.2 mmol O₂/l/min) that was comparable to or higher than those obtained in conventional flasks aerated by shaking. Direct aeration in combination with shaking resulted in OAR values that were elevated and most favorable for growth of oxygen demanding bacteria (5 mmol O₂/l/min). In comparison with controls, the direct method of aeration in combination with shaking proved most efficient and least dependent on the surface to volume ratio of the aerated solution. In experiments with the facultative anaerobe Streptococcus faecalis 10Cl, grown in controlled aerobic, anaerobic, and mixed gas (CO₂-free air, air-plus-CO₂, N₂-plus-CO₂) environments, a specific anaerobic requirement for CO₂ could be established. The wide range of gaseous environments possible renders the newly tested flask useful for comparative biochemical studies, especially when the gaseous condition of culture is a factor of critical importance.     

Enzymatic activity of circular sortase A under denaturing conditions: An advanced tool for protein ligation

Staphylococcus aureus sortase A is a transpeptidase that is extensively used in various protein research applications. Sortase A is highly selective and does not require any cofactors for the catalysis of protein ligation and, importantly, can be produced in high yields. However, the primary disadvantage of this transpeptidase is its inability to access the recognition site within the highly structured regions of folded substrates. To overcome this problem, we developed an Escherichia coli expression system that produces milligram quantities of circularly closed sortase A; efficient enzyme cyclization was achieved by Synechocystis sp. PCC6803 intein-mediated post-translational splicing. The structural integrity of circular sortase A and its biochemical characteristics were compared to those of the linear enzyme analog and were found to be similar under native conditions. Additionally, the modified sortase was active at concentrations of urea up to 3 M and was capable of efficient catalytic protein–protein coupling, as shown by the ligation of purified glutathione-S-transferase and green fluorescence protein. In contrast to the circular enzyme, linear sortase A was unable to mediate the ligation of substrate proteins under the same conditions. Therefore, the proposed circular sortase A has improved enzymatic properties and has applications in advanced protein engineering and design.     

极端条件下异养硝化-好氧反硝化菌脱氮的研究进展

异养硝化-好氧反硝化(HN-AD)是对传统自养硝化异养反硝化理论的丰富与突破。HN-AD菌在好氧条件下可快速实现氨氮、硝态氮(NO_3~–-N)、亚硝态氮(NO_2~–-N)三氮同步脱除。它们不仅具有分布范围广、适应能力强、代谢通路特殊等特点,而且还具有世代时间短、脱氮速率快、高活性持久等独特优势,在高盐、低温、高氨氮等极端条件表现出了巨大的脱氮潜力,因此在废水生物脱氮领域受到广泛关注。文中在介绍HN-AD菌属类别及代谢机理的基础上,重点总结了在高盐、低温、高氨氮等极端条件下进行氨氮脱除的HN-AD种属,系统分析了它们在极端条件下的脱氮特性及潜力,并简述了HN-AD菌在极端条件下的工艺应用研究进展,最后展望了HN-AD脱氮技术的应用前景和研究方向。     

Humus profiles of Siberian soils under different forming conditions

Humus profiles of Siberia soils under different conditions and models of soil formation are considered in the paper. It is shown that the humus profiles of soils formed in the regions of displacement of landscape and soil borders and developed according to the polygenetic model as well as the soils of synlithogenous type of pedogenesis have a complicated structure. Simple structure of the humus profile characterizes soils developing within the framework of a simple (ideal, normal) model of soil formation.     

Isolation of bacteria producing siderophores under alkaline conditions

Summary The isolation of bacteria producing siderophores under alkaline conditions is reported. Enrichment cultures initiated with samples from a number of alkaline environmental sources yielded 80 isolates. From this group selections were made on the basis of growth at high pH and the gallium-binding capacity of the siderophores. It was found that some isolates grew well and high concentrations of siderophore were detected whereas others grew well in the presence of much lower concentrations of siderophore. The effect of iron, gallium and aluminium on growth and siderophore production in batch culture was investigated for six isolates. The presence of iron greatly decreased the siderophore concentration in these cultures, whereas the response to added gallium or aluminium was dependent upon the isolate. Offsprint requests to: D. J. Gascoyne     

Diffusion profiles in L. lactis biofilms under different conditions

Despite being an important topic in biofilm research, we still know little about diffusion in biofilms. Emerging biofilms of Lactococcus lactis growing in custom‐made flow‐cells were monitored and diffusion constants across the height of the biofilms recorded. The biofilms showed different diffusional behavior with regard to flow rate and pH variations, despite growing to similar thickness. At a higher flow rate, the biofilm exhibits slower diffusion compared to the reference cultivation at lower flow rate. By increasing pH, the biofilm exhibited fast growth and little difference in diffusion compared to the reference cultivation. Furthermore, the diffusion inside of the biofilms differed depending on the position in the flow‐cell. The present study reveals new insights in how external factors can affect structure and density of biofilms. The method can be reliably used for L. lactis biofilms with a thickness up to 120 μm.     

Dominant fungi in the rhizosphere of established tea bushes and their interaction with the dominant bacteria under in situ conditions.

Species of Penicillium and Trichoderma were found to dominate the rhizosphere of established tea bushes in a detailed study conducted from various tea growing locations in India. Penicillium erythromellis, P. janthinellum, P. raistrickii, Trichoderma pseudokoningii and T. koningii were found to be closely associated with tea roots. While seasonal fluctuation was observed in the case of Penicillium spp., the population of Trichoderma spp. showed less variation during the year. Both species were sensitive to low temperatures. In general, fungi associated with the tea rhizosphere were found to prefer a mesophillic temperature range (15 °C to 35 °C). The dominant species of Penicillium and Trichoderma also exhibited tolerance to lower temperatures, i.e., 5 to 10 °C on agar plates. Most fungi were able to grow in a wide range of pH (4 to 12). Lowering of soil pH in the rhizosphere of tea bushes was positively correlated with the age of the bush and may have affected the development of a specific microbial community in the rhizosphere.

The populations of Penicillium and Trichoderma species were inversely correlated with the populations of two most dominant rhizosphere bacteria, Bacillus subtilis and B. mycoides. Both Bacillus species have been shown to have antagonistic activity against these two fungi under in vitro conditions. The present study demonstrates the existence of a similar antagonism under in situ conditions in the rhizosphere of established tea bushes.