深海微生物高压适应与生物地球化学循环

深海是典型的高压环境,嗜压微生物是深海生态系统中的重要类群.随着深海采样技术的发展及高压微生物特殊培养设备的开发,已从深海环境中分离到一系列嗜压微生物,包括一些常压环境不能生长的严格嗜压菌.对这些嗜压菌的研究,不仅对微生物适应极端高压环境的机制有一定了解,而且发现了一些特殊的代谢产物.研究微生物高压嗜压机理,还有助于探索地球生命的温度压力极限及生命起源和演化等科学问题.从深海嗜压微生物多样性、深海微生物高压环境适应机理及深海微生物在生物地球化学循环中的作用等方面对嗜压微生物的研究进展进行综述.     

油藏微生物及其压力适应机制

目前我国油田开发主要处于高含水后期,微生物驱提高石油采收率技术(MEOR)以低成本、环境友好等独特的优势引起了石油工业界的重视。实际上,经过半个多世纪的发展,MEOR已经成为提高采收率的重要前沿技术。高压是油藏的主要环境特征,在影响油藏微生物生存与活性等方面具有重要作用。本文从油藏及其微生物的主要特征、微生物对高压环境的适应机制以及高压下微生物降解烃的代谢特征等方面进行了综述。介绍了对油藏微生物资源、群落结构、微生物在油水相中分布的认识,微生物乳化原油机制,以及微生物在油藏厌氧环境中协同代谢、受温度和压力影响的特点,并列举了MEOR的矿场应用。在高压适应机制上,微生物主要通过改变和调整细胞膜结构、增加胞内脂质组分和表达胞内特殊酶等作用来实现对压力的适应;在高压下烃降解微生物代谢速率低于常压,而且耐压菌和嗜压菌具有不同的烃降解效率。     

Influence of osmoregulation processes on starvation survival of Escherichia coli in seawater.

The adaptation of enteric bacteria in seawater has previously been described in terms of nutrient starvation. In the present paper, we bring experimental arguments suggesting that survival of these microorganisms could also depend on their ability to overcome the effects of osmotic stress. We analyzed the influence of osmoregulatory mechanisms (potassium transport, transport and accumulation of organic osmolytes) on the survival of Escherichia coli in seawater microcosms by using mutants lacking components of the osmotic stress response. Long-term protection was afforded to cells by growth in a medium whose osmotic pressure was increased by either NaCl, LiCl, or saccharose. Achievement of the protection state depended at least partly on osmoregulatory mechanisms, but differed when these were activated or induced during prior growth or in resting cells suspended in phosphate buffer or in seawater. When achieved during growth, K+ transport, glycine-betaine (GBT) synthesis or transport, and trehalose synthesis helped increase the ability to survive in seawater. Protection by GBT was also obtained with resting cells in a phosphate buffer at high osmotic pressure. However, when added only to the seawater, GBT did not change the survival ability of cells no matter what their osmoregulation potential. These results showed that the survival of E. coli cells in seawater depends, at least partly, on whether they possess certain genes which enable them to regulate osmotic pressure and whether they can be stimulated to express those genes before or after their release into the environment. This expression requires nutrients as the substrates from which the corresponding gene products are made.     

Human diseases as representation of interspecies competition

Different aspects of competition between human and pathogenic microorganisms as well as their role in evolution of the human as biological species and development of its polymorphism were reviewed. Biological consequences of interaction between human and pathogenic microorganisms and also main factors of genetic selection such as tuberculosis, malaria, etc. were characterized. Numerous forms of polymorphism, which determine level of susceptibility and features of clinical course of many infections in humans, were described. It has been concluded that selective pressure of microorganisms results from direct selection due to excessive mortality of infected persons before integration in human genome as well as that immunologic pressure of mass immunization results in changes of pathogenic microorganisms populations leading to emergence of their antigenically distinct variants. New knowledge about competition between human and pathogenic microorganisms requires development of fundamentally new approaches in fight with infectious diseases.     

Effect of pressure assist on ventilation and respiratory mechanics in heavy exercise

To assess the effect of the normal respiratory resistive load on ventilation (VE) and respiratory motor output during exercise, we studied the effect of flow-proportional pressure assist (PA) (2.2 cmH2O.l-1.s) on various ventilatory parameters during progressive exercise to maximum in six healthy young men. We also measured dynamic lung compliance (Cdyn) and lung resistance (RL) and calculated the time course of respiratory muscle pressure (Pmus) during the breath in the assisted and unassisted states at a sustained exercise level corresponding to 70-80% of the subject's maximum O2 consumption. Unlike helium breathing, resistive PA had no effect on VE or any of its subdivisions partly as the result of an offsetting increase in RL (0.78 cmH2O.1-1.s) and partly to a reduction in Pmus. These results indicate that the normal resistive load does not constrain ventilation during heavy exercise. Furthermore, the increase in exercise ventilation observed with helium breathing, which is associated with much smaller degrees of resistive unloading (ca. -0.6 cmH2O.l-1.s), is likely the result of factors other than respiratory muscle unloading. The pattern of Pmus during exercise with and without unloading indicates that the use of P0.1 as an index of respiratory motor output under these conditions may result in misleading conclusions.     

High pressure processing for food safety

Food preservation using high pressure is a promising technique in food industry as it offers numerous opportunities for developing new foods with extended shelf-life, high nutritional value and excellent organoleptic characteristics. High pressure is an alternative to thermal processing. The resistance of microorganisms to pressure varies considerably depending on the pressure range applied, temperature and treatment duration, and type of microorganism. Generally, Gram-positive bacteria are more resistant to pressure than Gram-negative bacteria, moulds and yeasts; the most resistant are bacterial spores. The nature of the food is also important, as it may contain substances which protect the microorganism from high pressure. This article presents results of our studies involving the effect of high pressure on survival of some pathogenic bacteria -- Listeria monocytogenes, Aeromonas hydrophila and Enterococcus hirae -- in artificially contaminated cooked ham, ripening hard cheese and fruit juices. The results indicate that in samples of investigated foods the number of these microorganisms decreased proportionally to the pressure used and the duration of treatment, and the effect of these two factors was statistically significant (level of probability, P 相似文献   

Silent nucleotide substitutions and G+C content of some mitochondrial and bacterial genes

Summary The G+C content of DNA varies widely in different organisms, especially microorganisms. This variation is accompanied by changes in the nucleotide composition of silent positions in codons. (Silent positions are defined and explained in the text.) These changes are mostly neutral or near neutral, and appear to result from mutation pressure in the direction of increasing either A+T (AT pressure) or G+C(GC pressure) content. Variations in G+C content are also accompanied by substitutions at replacement positions in codons. These substituions produce changes in the amino acid content of homologous proteins. The examples studied were genes for 13 mitochondrial proteins in five species, and A and B genes for bacterial tryptophan synthase in four species.In microorganisms, varying AT and GC mutational pressures, presumably resulting from shifts in the DNA polymerase system, exert strong effects on molecular evolution by changing the G+C content of DNA. These effects may be greater than those of random drift. The effects of GC pressure on silent substitutions in the systems examined are several times as great as the effects on replacement substitutions.GC pressure is exerted on noncoding as well as coding regions in mitochondrial DNA. This is shown by the close correlation (correlation coefficient, 0.99) of the G+C content of the noncoding D loop of mitochondria with the G+C content of silent positions in the corresponding mitochondrial genes.     

Biorefinery products from the inulin-containing crop Jerusalem artichoke

The polysaccharides in Jerusalem artichoke (JA) carry a substantial amount of energy that can be partly accessed through bioconversion into storable fuels. We review the potential for converting inulin into a variety of high value-added biorefinery products, including biofuels and biochemicals, and consider the feasibility of regarding JA as a model species of an inulin-rich crop. We discuss feedstock pretreatment, microorganisms used during fermentation, biorefinery products derived from JA, and how to enhance the economic competitiveness of JA as an energy crop.     

Significance of the functional activity of toll-like receptors and other receptors of the innate immune system of the kidney physiology

The kidney needs to defend against microbial pathogens in order to maintain normal structure and function. This is achieved through innate and adaptive components of the immune system. For a long time, immunologists were concentrating on the adaptive immune system, which, as a result, was studied in detail; at the same time, the significance of the innate immune system was underestimated. This gap was partly filled in the recently, when the key role of the innate immune system in fighting microorganisms and in activating and regulating the adaptive immune system was convincingly established. In the first part of the present article, the sense apparatus of the innate immune system (the so-called pattern-recognition receptors) will be reviewed; particular attention will be paid to the toll-like receptors (TLRs), which bear the main burden of microorganism recognition. Signalling pathways that are activated by TLRs and result in the activation of effector mechanisms will also be reviewed. In the second part of the review, we will analyse available data on how these mechanisms of the innate immune system secure defence and normal functioning of the kidney.     

Metabolic Engineering for Microbial Production of Aromatic Amino Acids and Derived Compounds

Metabolic engineering to design and construct microorganisms suitable for the production of aromatic amino acids and derivatives thereof requires control of a complicated network of metabolic reactions that partly act in parallel and frequently are in rapid equilibrium. Engineering the regulatory circuits, the uptake of carbon, the glycolytic pathway, the pentose phosphate pathway, and the common aromatic amino acid pathway as well as amino acid importers and exporters that have all been targeted to effect higher productivities of these compounds are discussed.     

Agronomic and environmental aspects of diazotrophic bacteria in rice fields

This article provides an overview of the free-living and plant-associated nitrogen (N)-fixing bacterial communities in wet rice fields, with a focus on describing the elements affecting community assemblages in this waterlogged soil–plant system. Nitrogen is a crucial nutrient for rice yield and growth. Characteristics of the rice paddy ecosystem promote N-fertilizer losses, resulting in negative impacts on the environment. Public concerns on sustainable rice crop production and food security have accentuated interest in exploring biological supplementary nitrogen sources. Biological N-fixation is a significant source of the nitrogen in agroecosystems. The nitrogen requirement of rice crops can be partly remedied by managing and promoting the activities of N-fixing microorganisms. These changes are leading towards a cleaner approach that maintains sustainability while simultaneously improving crop production targets. The use of N-fixing microorganisms as biofertilizers and the factors driving the success of this technology in wet rice paddies are also discussed.     

Beyond the Matrix-Assisted Laser Desorption Ionization (MALDI) Biotyping Workflow: in Search of Microorganism-Specific Tryptic Peptides Enabling Discrimination of Subspecies

A well-accepted method for identification of microorganisms uses matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) coupled to analysis software which identifies and classifies the organism according to its ribosomal protein spectral profile. The method, called MALDI biotyping, is widely used in clinical diagnostics and has partly replaced conventional microbiological techniques such as biochemical identification due to its shorter time to result (minutes for MALDI biotyping versus hours or days for classical phenotypic or genotypic identification). Besides its utility for identifying bacteria, MS-based identification has been shown to be applicable also to yeasts and molds. A limitation to this method, however, is that accurate identification is most reliably achieved on the species level on the basis of reference mass spectra, making further phylogenetic classification unreliable. Here, it is shown that combining tryptic digestion of the acid/organic solvent extracted (classical biotyping preparation) and resolubilized proteins, nano-liquid chromatography (nano-LC), and subsequent identification of the peptides by MALDI-tandem TOF (MALDI-TOF/TOF) mass spectrometry increases the discrimination power to the level of subspecies. As a proof of concept, using this targeted proteomics workflow, we have identified subspecies-specific biomarker peptides for three Salmonella subspecies, resulting in an extension of the mass range and type of proteins investigated compared to classical MALDI biotyping. This method therefore offers rapid and cost-effective identification and classification of microorganisms at a deeper taxonomic level.     

The dual role of microbes in corrosion

Corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. It is a world-wide problem with great societal and economic consequences. Current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. Furthermore, they are rather inefficient. Therefore, there is an urgent need for environmentally friendly and sustainable corrosion control strategies. The mechanisms of microbially influenced corrosion and microbially influenced corrosion inhibition are not completely understood, because they cannot be linked to a single biochemical reaction or specific microbial species or groups. Corrosion is influenced by the complex processes of different microorganisms performing different electrochemical reactions and secreting proteins and metabolites that can have secondary effects. Information on the identity and role of microbial communities that are related to corrosion and corrosion inhibition in different materials and in different environments is scarce. As some microorganisms are able to both cause and inhibit corrosion, we pay particular interest to their potential role as corrosion-controlling agents. We show interesting interfaces in which scientists from different disciplines such as microbiology, engineering and art conservation can collaborate to find solutions to the problems caused by corrosion.     

Potato pulp: microbiological characterization, physical modification, and application of this agricultural waste product

Potato pulp, one of the agricultural waste products obtained in high quantities during starch production, contains starch, cellulose, hemicelluloses, pectin, proteins, free amino acids and salts. It exhibits physical and physicochemical properties of a typical colloid. It is mainly used, in a dried and pelleted form, as cattle feed. Its autochthonic microbial flora (bacteria, fungi) was identified and studied with a view towards the degradative potential of the microorganisms and ways of conserving the pulp for subsequent technical applications; 33 isolates (28 bacteria, 4 fungi, 1 yeast), belonging to 15 genera were characterized. Biological conservation was possible at very low oxygen pressure, brought about by the autochthonic anaerobic microorganisms causing acidification. Chemical conservation was achieved with sorbic aicd. By treatment with hot water vapour under pressure (autoclaving), followed by a pressure release procedure, intact cells in the pulp (both potato cells and microorganisms, not spores) were destroyed, and their contents and wall fragments were set free. This process resulted in low drying costs and was a prerequisite for the production of a powder that can be used as glue or as animal feed. Received: 18 April 1997 / Received revision: 12 June 1997 / Accepted: 14 June 1997     

High pressure processing of foods for microbiological safety and quality (a short review)

Consumers are demanding foods that are "natural", of good nutritional and sensory quality, free from chemical preservatives, microbiologically safe and with extended shelf-life. High pressure processing can, potentially, meet these criteria. Recent advances in equipment design now allow foods to be processed up to 900 MegaPascals (130,000 psi). However, further work is required to more fully understand the factors that can affect the response of microorganisms, including pathogens, to pressure so that treatments can be optimised and microbiological safety can be assured. This paper describes how the pressure resistance of microorganisms can vary depending on factors such as species, strain, stage of growth and food composition. Strategies for overcoming the problem of pressure resistance will be discussed, for example the use of pressure cycling and the combination of pressure with mild heat. The current commercial uses of high pressure to preserve foods will be reported and potential applications will also be discussed.     

Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and relocated in the environment as a result of the incomplete combustion of organic matter. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher systems including humans. Although various physicochemical methods have been used to remove these compounds from our environment, they have many limitations. Xenobiotic-degrading microorganisms have tremendous potential for bioremediation but new modifications are required to make such microorganisms effective and efficient in removing these compounds, which were once thought to be recalcitrant. Metabolic engineering might help to improve the efficiency of degradation of toxic compounds by microorganisms. However, efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by optimizing certain factors such as bioavailability, adsorption and mass transfer. Chemotaxis could also have an important role in enhancing biodegradation of pollutants. Here, we discuss the problems of PAH pollution and PAH degradation, and relevant bioremediation efforts.     

Fluid Dynamics Simulating Experiment of Pressure Gradient for Assimilate Translocation in Sieve Tubes

According to the similitude theory of fluid mechanics, a pressure-driven experiment in a sieve tube model has been performed. The relationships between the pressure gradient and the transport velocities at the various diameters of sieve pore have been obtained. The experimental data were compared with the theoretical prediction based on the poiseuille equation. The result shows that the pressure gradient required for translating the assimilate is directly proportional to the translating velocity, which agrees with Poiseuille equation. However, the resistance of the sieve plate to flow is much more than that estimated by the previous theory. Even though the translating velocity is a normal level and the diameter of the sieve tube is a typical size, the pressure gradient required for flow is about 1 bar/m. It will increase sharply with the decrease of the diameter of sieve pore. The ratios of the pressure gradients measured in the test to that predicted by Poiseuille equation are about 2–4 for the five kinds of diameters of Sieve pore. Additionally, a simulating test of the pores being partly plugged has been performed. The result shows that the pressure gradients measured are greatly beyond the range that may be kept in plants. This study will be helpful to assess Munch hypothesis.     

An alternate method for estimation of cell growth kinetics from batch cultures

An alternative to estimation of cell growth kinetics via continuous culture experiments is proposed in this article. The method employed is based on batch culture experiments with very small inocula (initial cell concentrations being typically less than 5000 cells/mL). Such low initial cell concentrations result in extended exponential cell growth phase during which culture conditions remain unchanged, thereby permitting precise estimation of specific cell growth rates from batch experiments especially for fast-growing microorganisms such as Bacillus species. The effectiveness and utility of this approach are demonstrated via several experiments conducted with a wild-type strain (Bacillus subtilis TN106) and a recombinant strain (B. subtilis TN106[pAT5]). True establishment of exponential growth phase requires insignificant variance of most of the culture conditions during the initial growth phase. Satisfaction of this requirement is demonstrated for microbial systems investigated here. This approach is especially well suited for recombinant microorganisms containing segregationally unstable plasmids, since estimation of growth kinetics of these from continuous cultures is very difficult and highly unreliable due to continual reversion of recombinant ceils to plasmid-free host cells unless some selection pressure is applied at levels sufficient to keep the presence of plasmid-free cells minimal.