发酵过程多尺度解析与调控的研究进展

工业发酵科学致力于实现高产量、高转化率和高生产强度的相对统一。通过从分子、细胞和反应器进行发酵过程多尺度解析与调控,实施全局与动态的优化与控制能够确保发酵过程高效、转化定向、过程稳定和系统有序。本文从发酵微生物代谢途径动力学模型、细胞代谢特性、发酵提取相耦合与反应器设计四个方面,总结和讨论发酵过程多尺度解析与调控的研究进展。整合分析发酵过程不同尺度特征并且针对性地开展多尺度整合调控是实现高效工业微生物发酵的重要策略。     

Image analysis for monitoring the barley tempeh fermentation process

AIMS: To develop a fast, accurate, objective and nondestructive method for monitoring barley tempeh fermentation. METHODS AND RESULTS: Barley tempeh is a food made from pearled barley grains fermented with Rhizopus oligosporus. Rhizopus oligosporus growth is important for tempeh quality, but quantifying its growth is difficult and laborious. A system was developed for analysing digital images of fermentation stages using two image processing methods. The first employed statistical measures sensitive to image colour and surface structure, and these statistical measures were highly correlated (r=0.92, n=75, P<0.001) with ergosterol content of tempeh fermented with R. oligosporus and lactic acid bacteria (LAB). In the second method, an image-processing algorithm optimized to changes in images of final tempeh products was developed to measure number of visible barley grains. A threshold of 5 visible grains per Petri dish indicated complete tempeh fermentation. When images of tempeh cakes fermented with different inoculation levels of R. oligosporus were analysed the results from the two image processing methods were in good agreement. CONCLUSION: Image processing proved suitable for monitoring barley tempeh fermentation. The method avoids sampling, is nonintrusive, and only requires a digital camera with good resolution and image analysis software. SIGNIFICANCE AND IMPACT OF THE STUDY: The system provides a rapid visualization of tempeh product maturation and qualities during fermentation. Automated online monitoring of tempeh fermentation by coupling automated image acquisition with image processing software could be further developed for process control.     

Model aided dynamic process analysis and optimization for the nourseothricin fermentation

The relation between product formation and growth kinetics could be characterized by two facts: the specific product formation rate depends on the ageing of the population and on the specific growth rate. These relation was formulated and quantified by a mathematical model, which was fitted to experimental data of a representative fermentation run und used to predict an optimal fermentation mode. In the result of this discussion cyclic fed batch fermentation was found to be optimal.     

Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae

The fed-batch fermentation of glycerol to 1,3-propanediol by Klebsiella pneumoniae displayed an unusual dynamic behavior that can be clearly divided into four distinct phases according to cell growth and CO(2) evolution rate. Metabolism changed significantly during the different phases as reflected by the varied specific rates of substrate consumption and product formation. An assay of activities of the three initial enzymes of glycerol metabolism, namely glycerol dehydratase (GDHt), glycerol dehydrogenase (GDH), and 1,3-propanediol-oxidoreductase (PDOR), showed apparently different patterns of expression. To understand the culture dynamics and patterns of enzyme formation at a more systemic level we analyzed the expression patterns of intracellular proteins of K. pneumoniae from different phases of the fed-batch fermentation using two-dimensional gel electrophoresis (2DE). Two new enzymes, namely a phosphoenolpyruvate-dependent dihydroxyacetone kinase (DHAK II) and a hypothetical oxidoreductase (HOR), which are directly related to glycerol metabolism and 1,3-propanediol formation, were identified among the highly expressed proteins. The changes in expression of these new enzymes and several other proteins identified from the 2DE analysis helped to understand not only the dynamic behavior of the fed-batch fermentation reported in this work but also some previously insufficiently understood phenomena related to this fermentation process. In particular, we demonstrated the combined use of proteomic analysis and enzyme activity assay data for metabolic pathway analysis and for a better identification of targets for bioprocess improvement.     

High-productivity fermentation process for cultivating industrial microorganisms

Summary High-productivity continuous fermentation processes have been developed for the production of important industrial microorganisms in specially designed fermentors.Saccharomyces cerevisiae, Pichia pastoris, Kluyveromyces fragilis, andCandida utilis yeasts have been grown in bench-scale fermentors at cell densities of over 120 g/l, whileEscherichia coli, Bacillus megaterium, Methylomonas sp. andPseudomonas putida bacteria have been cultivated to cell densities of more than 110 g/l. Productivities (g cells per 1 per h) greater than 25 have been achieved in both bench-scale and 1500-liter fermentors with yeasts, and values as high as 55 have been achieved with bacteria in the bench-scale fermentor. The microorganisms were grown on defined media using ammonia for pH control and as nitrogen source. The fermentor, capable of high oxygen and heat transfer rates, was operated at constant volume with continuous feed and product discharge. The high-productivity process reduces fermentor size, media sterilization requirements, and may under some circumstances eliminate waste and recycle streams. It can also be applied to a variety of biological products.     

Measurement error in heat tolerance assays

Biological measurements inherently involve some measurement error (ME), which is a major concern because measurement accuracy (how closely a measurement reproduces the true value of the attribute being measured) and statistical power steadily decrease with increasing ME. However, ME has been largely overlooked in the thermal biology literature, which can be explained by the fact that thermotolerance estimates often involve the collapse or death of the tested individuals and measurements cannot be repeated in vivo with the same specimen under identical conditions. Here we assess inter- and intra-researcher (test-retest) reliability of heat tolerance measured as knockdown time from digital recordings of Drosophila subobscura flies individually assayed in vials with a dynamic method. We provide a summary of various estimators used to compute measurement reliability (the degree to which the measurement is affected by ME) together with their statistical properties. Our results indicate that the estimation of heat knockdown time has poor reliability: intra-researcher ME=29% and inter-researcher ME=34%. This difference is attributed to lack of ‘accurateness’ (the difference in the marginal distributions of the measurements taken by the two researchers) because measurement imprecision was essentially the same in both estimates (27%). In view of our results we conclude that thermal biologists should report the reliability of thermotolerance estimates and, when necessary, adopt some straightforward guidelines suggested here to improve measurement reliability.     

Periodic-peristole agitation for process enhancement of butanol fermentation

Background

Mass transfer plays an important role in determining the efficiency of the biofuel conversion. However, adverse effect of shear stress from traditional agitation inhibits the cell growth and production of biofuels. How to enhance the mass transfer with less adverse effect is considered as one of the important bioengineering issues.

Results

In this study, a novel agitation type, named periodic-peristole was applied to butanol fermentation with Clostridium acetobutylicum ATCC 824. Meanwhile, the enhancement mechanism was studied. Initially, the fermentation performance of periodic-peristole agitation was compared with the traditional Rushton impeller and stationary cultivation. Result showed that the biomass, butanol and total solvent in periodic-peristole group (PPG) was enhanced to 1.92-, 2.06-, and 2.4-fold of those in the traditional Rushton impeller group (TIG), as well as 1.64-, 1.19- and 1.41-fold of those in the stationary group (SG). Subsequently, to get in-depth insight into enhancement mechanism, hydromechanics analysis and metabolic flux analysis (MFA) were carried out. The periodic-peristole agitation exhibits significant difference on velocity distribution, shear force, and mixing efficiency from the traditional Rushton impeller agitation. And the shear force in PPG is only 74 % of that in TIG. According to MFA result, fructose 6-phosphate, pyruvate, acetyl-CoA, oxaloacetate and α-ketoglutarate were determined the key nodes of cells in response to hydrodynamic mechanical stress. Based on such key information, rational enhancement strategies were proposed and butanol production was further improved.

Conclusion

The agitation associated with three issues which resulted in significant changes in cell metabolic behaviors: first, a rebalanced redox status; second, the energy (ATP) acquirement and consumption; third, the tolerance mechanism of the cell for survival of solvent. Periodic-peristole agitation provides an answer to address a long-standing problem of biofuel engineering. Key information derived from current study deepens the understanding of agitation, which can guide the designment of new bioreactors and development of enhancement strategies for biofuel refinery.

     

S-腺苷-L-蛋氨酸高密度发酵工艺优化

利用酿酒酵母在5L发酵罐高密度发酵生产S-腺苷-L-蛋氨酸(SAM)后期存在稳定性差的问题,本研究考察了在补糖中添加磷酸氢二铵、谷氨酸钠、三磷酸腺苷二钠来提高酿酒酵母发酵后期的稳定性。通过4批5L发酵罐高密度流加发酵实验研究发现:在发酵34h左右,菌体干重超过100g/L后,开始添加50克L-蛋氨酸,并在补糖中加入10g/L三磷酸腺苷二钠,发酵65.7h,最高生物量干重达到180g/L,SAM产量达到17.1g/L。     

Rapid antibody biosensor assays for environmental analysis

Traditionally, biosensor development has focused on molecules with a defined metabolic role that can be exploited by enzyme-based systems. Antibodies have the ability to move beyond this range of analytes, and are particularly useful in detecting small, hapten molecules. Electrochemically based biosensor developments have been less fruitful in this regard, as enzyme labelling is required, and such assays require the separation from bound and unbound species. These separations and the removal of background signals result in the increased complexity of the assay format, making it unsuitable for rapid sensor analysis. We have developed an electrochemical sensor based on antibodies that does not require the separation of bound and unbound molecules in a competition immunoassay format. This removes the need for several washing and separation steps as is normally employed in this type of assay. This allows single-step immunoassays to be performed using this system, and also allows for the real-time monitoring of antibody-antigen interactions. We have shown that such assays are possible in both batch and flow-injection formats and we are currently developing an assay for the pesticide atrazine. Tentative results show that analysis with this system is possible in the p.p.m. to p.p.b. range.     

初始条件对高浓度乙醇连续发酵过程的影响及振荡行为提高发酵效率的机理分析

前期实验在稀释速率为0.027h-1的高浓度乙醇连续发酵过程中,发现了一种长周期、宽振幅的参数振荡现象。本实验进一步考察了不同稀释速率下的连续发酵过程,发现在稀释速率为0.04h-1条件下,也能出现类似的振荡现象;在稀释速率为0.027h-1或0.04h-1的条件下,改变系统的初始状态可以得到振荡和稳态两种不同的发酵过程。比较振荡和稳态过程的实验数据后,发现在稀释速率为0.04h-1的条件下,与稳态过程相比,振荡过程的平均残糖浓度降低了14.8%,平均乙醇浓度提高了12.6%,平均设备生产强度提高了12.3%。进一步分析表明:与稳态过程相比,振荡过程动力学行为不仅存在滞后,而且在相同残糖和乙醇浓度条件下,所对应的平均比生长速率提高了53.8%。     

Wine-making by cell-recycle-batch fermentation process

Summary In order to check the overall validity of more efficient fermentation systems to reduce wine-making costs, we carried out an off-skins fermentation of clarified Trebbiano toscano grape-juice, making use of a non-conventional cell-recycle-batch fermentation process. The results showed that the process causes a reduction of the fermentation length as well as an improvement in ethanol productivity and yield and can be conveniently applied to the production of ordinary table wines.This work was supported in part by a grant from the Italian C.N.R. (Consiglio Nazionale delle Ricerche)     

Bifurcation analysis of a product inhibition model of a continuous fermentation process

Summary A product inhibition model of a continuous fermentation process is considered. If the yield term is a variable function of ethanol concentration, oscillation in the cell and ethanol concentrations is shown to be a Hopf bifurcation in the underlying system of nonlinear, ordinary differential equations which comprises the model.     

裂殖壶菌发酵产DHA过程呼吸参数的在线检测分析

利用尾气分析仪对发酵过程的尾气中的O2、CO2含量进行实时检测,建立了裂殖弧菌发酵生产DHA过程中的呼吸参数在线检测方法,实现了裂殖壶菌补料分批发酵过程及双阶段供氧控制发酵过程中的呼吸参数在线检测分析。通过呼吸参数在线检测分析,从氧消耗机制方面解释了双阶段氧传递控制工艺能获得较高生物量、油脂和DHA含量的原因,从而为该工艺过程提供了理论指导。根据发酵过程中菌体生长不同时期的呼吸参数的变化情况,建立了基于呼吸商变化的在线补料控制方法,设计了一种基于RQ-Stat的补料工艺。RQ-Stat补料方式最终获得的油脂含量、DHA产量和产率比间歇式补料工艺分别提高了11.58%、12.19%和11.40%。     

谷氨酸发酵过程葡萄糖自动流加系统

补料（流加葡萄糖）操作是谷氨酸发酵过程最重要的操作之一,工业上有各种各样的补料操作方法。控制葡萄糖浓度于一个较为平稳且适中的水平有利于提高谷氨酸发酵的性能指标。通过在线计量谷氨酸发酵中的氨水耗量并据此在线推定发酵液中的葡萄糖浓度,构建了一个谷氨酸发酵自动在线补料系统。使用该控制系统,谷氨酸发酵过程的葡萄糖浓度可以控制在任意水平,平稳、无波动的谷氨酸发酵可以得到实现。     

FPC-ICAD: an intelligent CAD for fermentation process control

The paper presents an Intelligent CAD system for Fermentation Process Control (FPC-ICAD) based on a hierarchical architecture possessing three levels: real-time supervision level, CAD level and learning level. The aims of the learning are mainly composed of the aspects fermentation process modelling, determination of appropriate control and estimation methods, determination of the corresponding parameters and fermentation monitoring through measurement and software management. Three independent, but interactive software packages allow user to organize his system for different purposes: on-line control system (with only supervision), off-line CAD as a teaching software, off-line intelligent CAD (CAD+learning package), and on-line intelligent CAD.     

The cocoa bean fermentation process: from ecosystem analysis to starter culture development

Cocoa bean fermentation is still a spontaneous curing process to facilitate drying of nongerminating cocoa beans by pulp removal as well as to stimulate colour and flavour development of fermented dry cocoa beans. As it is carried out on farm, cocoa bean fermentation is subjected to various agricultural and operational practices and hence fermented dry cocoa beans of variable quality are obtained. Spontaneous cocoa bean fermentations carried out with care for approximate four days are characterized by a succession of particular microbial activities of three groups of micro‐organisms, namely yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), which results in well‐fermented fully brown cocoa beans. This has been shown through a plethora of studies, often using a multiphasic experimental approach. Selected strains of several of the prevailing microbial species have been tested in appropriate cocoa pulp simulation media to unravel their functional roles and interactions as well as in small plastic vessels containing fresh cocoa pulp‐bean mass to evaluate their capacity to dominate the cocoa bean fermentation process. Various starter cultures have been proposed for successful fermentation, encompassing both cocoa‐derived and cocoa nonspecific strains of (hybrid) yeasts, LAB and AAB, some of which have been implemented on farms successfully.     

Application of bead-based assays for flow cytometry analysis

To date microsphere-based assays in flow cytometry have focused on the detection of antibody or antigen. Most studies have been research based to evaluate the performance of the technique relative to conventional techniques. However, there have not been any carefully controlled studies of the sensitivity and specificity, as well as analytic sensitivity of the FMIA technique. As such, it is difficult to document advantages of this tecnique clearly. The data suggest that FMIA is considerably more sensitive than conventional techniques, and the ability to analyze for multiple analytes in one sample dilution is attractive. This ability to simultaneously analyze for multiple samples is primarily dependent upon the size difference as sensed by FALS of the microspheres. However, it is also possible to use microspheres of the same size but that differ in either fluorescence or RALS signal. If microspheres of the same size are used but one fluoresces red and the signal in the assay uses a green fluorochrome, then the two microspheres can be separated by their red fluorescence. Using this technique, one can increase the number of microspheres that can be used in an assay. It is also possible to use microspheres of the same size but with different abilities to scatter the incident light at right angles. The use of these microspheres is then similar to the nonfluorescent versus red microspheres. By the judicious combination of microsphere size, it is possible to easily differentiate eight different microspheres. With the addition of a fluorescebt dye and/or differences in right-angle light-scatter capabilities, the number of different microspheres that can be used simultaneously becomes quite large. In practice, the number of microspheres that can be differentiated is no doubt greater than the number of analytes that need to be assayed in one assay.Although the apparent increase in sensitivity and the ability to simultaneously detect and quantitate numerous analytes are important attributes of FMIA, there are drawbacks to this method. Although the FMIA lends itself well to one-step no-wash procedures, when wash steps are necessary they are time-consuming and ineffecient. Most wash steps in FMIA use centrifugation of the microspheres to remove them from the reagent. There is a significant loss of microspheres in these wash steps, which are time-consuming. There are studies ussing vacuum filtration of the suspension to separate the microspheres from the reagents. A number of different groups are pursuing an automated or semiautomated method for the efficient washing and reagent delivery system for FMIA. Commercial systems are being developed that may allow for the easier handling of these reagents.Numerous groups are investigating the use of microspheres and flow cytometry primarily in immunoassay development. The procedure has the advantages of the simultaneous yet discrete analysis of multiple analytes and the inherent increase in sensitivity using fluorescence over other signals. There will no doubt be wider applications     

An innovative consecutive batch fermentation process for very high gravity ethanol fermentation with self-flocculating yeast

An innovative consecutive batch fermentation process was developed for very high gravity (VHG) ethanol fermentation with the self-flocculating yeast under high biomass concentration conditions. On the one hand, the high biomass concentration significantly shortened the time required to complete the VHG fermentation and the duration of yeast cells suffering from strong ethanol inhibition, preventing them from losing viability and making them suitable for being repeatedly used in the process. On the other hand, the separation of yeast cells from the fermentation broth by sedimentation instead of centrifugation, making the process economically more competitive. The VHG medium composed of 255 g L⁻¹ glucose and 6.75 g L⁻¹ each of yeast extract and peptone was fed into the fermentation system for nine consecutive batch fermentations, which were completed within 8–14 h with an average ethanol concentration of 15% (v/v) and ethanol yield of 0.464, 90.8% of its theoretical value of 0.511. The average ethanol productivity that was calculated with the inclusion of the downstream time for the yeast flocs to settle from the fermentation broth and the supernatant to be removed from the fermentation system was 8.2 g L⁻¹ h⁻¹, much higher than those previously reported for VHG ethanol fermentation and regular ethanol fermentation with ethanol concentration around 12% (v/v) as well.     

Real-time optimisation of a fermentation process

An adaptive on-line sub-optimal control system for yeast fermentation was developed. The control package is described with a brief history of progress. Results show the effect of the control package on process variables, and indicate present limitations and future development.