Kinetics of multiproduct acidogenic and solventogenic batch fermentations

Summary Large amounts of data indicated that most of the metabolic processes of the acidogenic (acid producing) and the solventogenic (solvent producing) fermentations were regulated by product accumulation. A simple unstructured model simulated microbial growth, product formation and substrate utilization in six different fermentations, where five different microorganisms produced various combinations of ten different products. Specific growth rates of these microorganisms decreased proportionally with overall product accumulation. The products were excreted in non-growth associated pattern. Excretion of some of these products were inhibited by the overall product accumulation similarly as the microbial growth. A substrate consumption model which considered the biomass and individually all the products as separate substrate sinks simulated the data satisfactorily.     

Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth.

Schr?dinger stated in his landmark book, What is Life?, that life feeds on negative entropy. In this contribution, the validity of this statement is discussed through a careful thermodynamic analysis of microbial growth processes. In principle, both feeding on negative entropy, i.e. yielding products of higher entropy than the substrates, and generating heat can be used by microorganisms to rid themselves of internal entropy production resulting from maintenance and growth processes. Literature data are reviewed in order to compare these two mechanisms. It is shown that entropy-neutral, entropy-driven, and entropy-retarded growth exist. The analysis of some particularly interesting microorganisms shows that enthalpy-retarded microbial growth may also exist, which would signify a net uptake of heat during growth. However, the existence of endothermic life has never been demonstrated in a calorimeter. The internal entropy production in live cells also reflects itself in the Gibbs energy dissipation accompanying growth, which is related quantitatively to the biomass yield. An empirical correlation of the Gibbs energy dissipation in terms of the physico-chemical nature of the growth substrate has been proposed in the literature and can be used to predict the biomass yield approximately. The ratio of enthalpy change and Gibbs energy change can also be predicted since it is shown to be approximately equal to the same ratio of the relevant catabolic process alone.     

熏蒸剂溴甲烷对农田土壤微生物的影响

土壤微生物是反应土壤健康状况最敏感的生物学指标,溴甲烷残留不仅消耗臭氧层,影响生态平衡,还会造成土壤质量恶化和微生物群落结构的变化。为明确溴甲烷对农田土壤微生物群落结构及生态过程的影响,以兰州市红古区连续两年种植草莓的土壤为研究对象,测定熏蒸剂溴甲烷处理后土壤微生物量碳、基础呼吸、诱导呼吸和微生物代谢熵等相关指标,并运用磷脂脂肪酸法(PLFA)测定不同类群微生物的变化。结果表明:经溴甲烷熏蒸处理至培养结束(第90天)时土壤微生物基础呼吸和诱导呼吸分别下降0.6%和16.2%,并且与对照皆差异显著(P 0.05);微生物量碳培养结束时与对照差异显著(P 0.05),且减少5.6%;总体上微生物基础呼吸、诱导呼吸和微生物量碳都呈现先下降后逐渐恢复的趋势;微生物代谢熵(q CO_2)第15天后都高于对照,但随培养时间延长,处理组和对照组的差值逐渐降低,到培养期结束仍未恢复,相差5.1%。溴甲烷对土壤细菌(B)、真菌(F)和革兰氏阴性菌(GN)、革兰氏阳性菌(GP)都存在抑制作用; B、F含量分别较对照下降0.64%—8.72%、0.03%—5.61%;到培养期结束时,GP的量下降0.26%,GN下降10.42%,GN对溴甲烷的敏感性强于GP,且GN的变化具有滞后性;溴甲烷处理降低了B/F和GN/GP,但对GN/GP影响比对B/F的更为显著,土壤微生物压力指数增加。综上,说明施用溴甲烷使农田土壤微生物受到了长期的、持续的外源压力胁迫,溴甲烷在对有害微生物杀死的同时,也对有益微生物造成极大的伤害,不利于土壤优良性状的保持,使土壤中微生物丰富度和多样性下降。因此,实际应用中应充分考虑溴甲烷对土壤微生物带来的负面影响。     

Agrichemical impact on growth and survival of non-target apple phyllosphere microorganisms

The impact of conventional agrichemicals commonly used in New Zealand apple production on non-target, culturable phyllosphere microbial populations was studied in the laboratory (agar, leaf, and seedling assays) and field (apple orchard). Morphologically distinct bacteria (three), yeasts (five), and filamentous microfungi (two) were used as indicator species. The agar assay showed that agrichemical toxicity to microorganisms was dependent on product type, product rate, and organism studied. While the fungicides metiram and captan stopped or severely reduced growth of nearly all microorganisms studied, the insecticides tebufenozide and lufenuron and the fungicide nitrothal-isopropyl showed the least amount of microbial toxicity, each affecting 2 of the 10 indicator organisms studied. In the leaf assay a single agrichemical application at field rate either reduced or increased microbial population counts, again depending on product and microorganism. Repeated agrichemical applications, however, reduced microbial population numbers from 10- to 10,000-fold in planta. Further field research validated these findings, although differences in microbial numbers before and after agrichemical applications were less dramatic. In the orchard, total organism numbers recovered within 2-6 days, but species richness (sum of recognizable taxonomic units) declined. Agrichemicals clearly affected non-target, culturable surface microorganisms. The importance of diversity and stability of microbial populations for disease control still needs to be established.     

Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms Lactobacillus plantarum, Lactococcus lactis, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus niger. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology.     

Production of natural value-added compounds: an insight into the eugenol biotransformation pathway

During the past few years, the production of natural value-added compounds from microbial sources has gained tremendous importance. Due to an increase in consumer demand for natural products, various food and pharmaceutical industries are continuously in search of novel metabolites obtained from microbial biotransformation. The exploitation of microbial biosynthetic pathways is both feasible and cost effective in the production of natural compounds. The environmentally compatible nature of these products is one major reason for their increasing demand. Novel approaches for natural product biogeneration will take advantage of the current studies on biotechnology, biochemical pathways and microbiology. The interest of the scientific community has shifted toward the use of microbial bioconversion for the production of valuable compounds from natural substrates. The present review focuses on eugenol biotransformation by microorganisms resulting in the formation of various value-added products such as ferulic acid, coniferyl alcohol, vanillin and vanillic acid.     

形态工程在生物基化学品生产中的应用进展

合成生物学和代谢工程是构建微生物细胞工厂、实现化学品绿色生物制造的重要方法,目前主要集中在微生物代谢网络的改造及调控上,很少考虑到微生物细胞特性的影响。形态工程通过改造微生物细胞形态相关蛋白,有目的地对微生物细胞形态及分裂方式进行合理调控,从而优化微生物细胞的特性,是降低生物炼制成本的一种新兴生物工程技术。文中首先介绍了与微生物细胞形态相关的各类蛋白,并重点总结了形态工程在生物基化学品合成方面的应用进展,包括调控细胞体积以提高胞内产物积累量、改善细胞通透性以促进胞外产物分泌、实现高密度发酵以降低生产成本、控制产物水解程度以提高产品性能。最后,提出了形态工程面临的主要问题并展望了其未来的发展趋势。     

Studies on formation,control and application of biofilm formed by food related microorganisms

Biofilms are sessile microbial aggregates on the interfaces, and they were usually considered as microbial contamination sources in medical care and various industries. We studied the control and application of biofilms formed by food-related microorganisms, and mechanism of the biofilm formation was also investigated. We studied the biofilm formation in mixed cultures using various combinations of two strains of food-related microorganisms. There were various microorganisms that showed decreased or increased biofilm formation in the mixed culture in comparison with that in a single culture. Biofilm formed by lactic acid bacteria and yeast isolated from traditional fermented food, Fukuyama pot vinegar, exhibited unique feature in that structure and formation mechanism, and expected to be used as an immobilized microorganism in fermentation production. Here our studies on the control and application of biofilms and the mechanisms of its formation were described.     

光照混菌培养应用研究进展

光合细菌与其他微生物在光照条件下混合培养是近年来的研究热点。综述了光照混菌培养的特点和目前光照混菌培养在水体净化、生物制氢和高价值物质生产方面的应用,并对影响混合菌株生长代谢与繁殖的因素做了总结。分析表明菌株之间存在的相互协同共生作用能促进微生物的生长繁殖,使底物被充分利用,提高物质产率。光照混菌培养工艺简单、成本较低,在水体净化、生物制氢、高价值物质生产方面的应用具有相当好的效果。在影响因素中对混合培养影响最大的因素是菌株接种量、接种比和培养基pH。在总结光照混菌培养应用现存不足的基础上,对其发展前景作出展望。     

Evaluation of a quantitative screening method for hydrogen sulfide production by cheese-ripening microorganisms: the first step towards l-cysteine catabolism

A practical adaptation of the methylene blue reaction for hydrogen sulfide quantification was developed to perform microbial selection. Closed plate flasks containing a zinc-agar layer above the liquid microbial culture are proposed as a trap system where the H(2)S can be retained and then quantified by the methylene blue reaction. Using this quantitative method, the ability to produce H(2)S was studied in several cheese-ripening microorganisms. Our aim was to select strains that produce the highest quantities of H(2)S as the main product of L-cysteine catabolism. Thirty seven yeast and bacteria strains were cultivated with or without L-cysteine. The separation between the growth medium and the H(2)S trapping layer displayed good performance: all the studied strains grew efficiently and only negligible loss of H(2)S was observed during culturing. The strains displayed large differences in their H(2)S production capabilities: yeast strains were greater producers of H(2)S than bacteria with production strain-related in both cases. Furthermore, the relationship between H(2)S production and L-cysteine consumption was analyzed, which made it possible for us to select microorganisms with high capacity in L-cysteine degradation. The production of volatile sulfur compounds was also studied and the possible effect of culture pH and metabolic differences between strains are discussed.     

Mini-review: microbial problems in paper production

Paper mills are open systems, which provide favorable conditions for microbial growth. Microbial contamination can cause substantial economic losses, including the deterioration of raw materials, interference with production processes by breakdowns and lowering product quality, and eventually, problems in wastewater treatment. Damage is caused by acidification, attack on raw materials, the formation of odorous products, discoloration of pigments, and the formation of methane and hydrogen, thereby producing potentially explosive conditions. Population analyses have revealed that a wide variety of microorganisms are involved, but there appear to be no typical strains associated with paper mills. Current trends in process engineering, such as chlorine-free bleaching, processing at neutral pH, closed cycles, and the use of recycled paper also favor microbial growth and biofilm (slime) formation. A fundamental problem associated with slimes is the extensive matrix of extracellular polymeric substances, which is composed of a large variety of highly hydrated polysaccharides, proteins, nucleic acids, and lipids. No ‘silver bullet’ against biofouling can be expected, and effective countermeasures have to be based on holistic approaches.     

Stability and Effects of Some Pesticides in Soil

The influence of 29 pesticides on CO(2) production and nitrification by soil microorganisms was determined. A few compounds were stable but without significant effect in soil (chlorinated hydrocarbons), some persisted and depressed respiration and nitrification (carbamates, cyclodienes, phenylureas, thiolcarbamates), and others displayed toxicity but were transformed by soil microorganisms (amides, anilides, organophosphates, phenylcarbamates, triazines). Some compounds of the last type induced an initial increase and subsequent decrease in CO(2) production by soil. No simple explanation of this effect is possible, but the results of studies of model systems having established activities suggest that in soil any one or a combination of the following mechanisms is responsible for the observed complex relation of CO(2) production to time: (i) a pesticide acts to uncouple oxidative phosphorylation in a manner analogous to 2,4-dinitrophenol; (ii) a pesticide lacking antimicrobial action is oxidized in part and transformed to a stable and toxic product; (iii) a pesticide that is selectively toxic inhibits CO(2) production by sensitive microorganisms but is subject to oxidation without detoxification by other members of the microbial population that are resistant to its initial action. Pesticide concentrations greatly in excess of those recommended for agricultural and home use were required to produce an effect, and supplementary organic matter (glucose) tended to reduce pesticide toxicity and increase the microbial degradation of pesticides in soil.     

耐受性工程调控微生物细胞工厂胁迫抗性

微生物细胞工厂的生产效率是由菌株生长性能、产品合成能力和胁迫抗性共同决定的,其中增强微生物细胞工厂的胁迫抗性是关键.耐受性工程基于微生物细胞工厂抵御胁迫压力的应激反应机制,通过巩固壁膜屏障增强胁迫防御能力,加快应激反应提高损伤修复能力,创制耐受进化工具筛选鲁棒性增强的工业微生物.文中分析归纳了耐受性工程的调控策略,并展...     

Suitable microscopic entropy for the origin of microbial life: Microbiological methods are challenges

A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.     

Application of macroscopic principles to microbial metabolism

General expressions for mass, elemental, energy, and entropy balances are derived and applied to microbial growth and product formation. The state of the art of the application of elemental balances to aerobic and heterotrophic growth is reviewed and extended somewhat to include the majority of the cases commonly encountered in biotechnology. The degree of reduction concept is extended to include nitrogen sources other than ammonia. The relationship between a number of accepted measures for the comparison of substrate yields is investigated. The theory is illustrated using a generalized correlation for oxygen yield data. The stoichiometry of anaerobic product formation is briefly treated, a limit to the maximum carbon conservation in product is derived, using the concept of elemental balance. In the treatment of growth energetics the correct statement of the second law of thermodynamics for growing organisms is emphasized. For aerobic heterotrophic growth the concept of thermodynamic efficiency is used to formulate a limit the substrate yield can never surpass. It is combined with a limit due to the fact that the maximum carbon conservation in biomass can obviously never surpass unity. It is shown that growth on substrates of a low degree of reduction is energy limited, for substrates of a high degree of reduction carbon limitation takes over. Based on a literature review concerning yield data some semiempirical notions useful for a preliminary evolution of aerobic heterotrophic growth are developed. The thermodynamic efficiency definition is completed by two other efficiency measures, which allow derivation of simple equations for oxygen consumption and heat production. The range of validity of the constancy of the rate of heat production to the rate of oxygen consumption is analyzed using these efficiency measures. The energetic of anaerobic growth are treated—it is shown that an approximate analysis in terms of an enthalpy balance is not valid for this case, the evaluation of the efficiency of growth has to be based on Gibbs free energy changes. A preliminary analysis shows the existence of regularities concerning the free energy conservation on anaerobic growth. The treatment is extended to include the effect of growth rate by the introduction of a linear relationship for substrate consumption. Aerobic and anaerobic growth are discussed using this relationship. A correlation useful in judging the potentialities for improvement in anaerobic product formation processes is derived. Finally the relevance of macroscopic principles to the modeling of bioengineering systems is discussed.     

Real-time monitoring and control of microbial bioprocesses with focus on the specific growth rate: current state and perspectives

Understanding the growth characteristics of microorganisms is an essential step in bioprocessing, not only because product formation may be growth-associated but also because they might influence cell physiology and thereby product quality. The specific growth rate, a key variable of many bioprocesses, cannot be measured directly and relies on the estimation through other measurable variables such as biomass, substrate, or product concentrations. Techniques for real-time estimation of the specific growth rate in microbial fed-batch cultures are discussed in the present paper. The advantages and limitations of different models and various monitoring techniques are discussed, highlighting the importance of the specific growth rate in the development of fast, reliable, and robust processes for the production of high-value products such as recombinant proteins.     

Importance of systems biology in engineering microbes for biofuel production

Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.     

Microbial diversity in support of anaerobic biomass valorization

Microbial diversity provides an immense reservoir of functions and supports key steps in maintaining ecosystem balance through matter decomposition processes and nutrient recycling. The use of microorganisms for biomolecule production is now common, but often involves single-strain cultures. In this review, we highlight the significance of using ecosystem-derived microbial diversity for biotechnological researches. In the context of organic matter mineralization, diversity of microorganisms is essential and enhances the degradation processes. We focus on anaerobic production of biomolecules of interest from discarded biomass, which is an important issue in the context of organic waste valorization and processing. Organic waste represents an important and renewable raw material but remains underused. It is commonly accepted that anaerobic mineralization of organic waste allows the production of diverse interesting molecules within several fields of application. We provide evidence that complex and diversified microbial communities isolated from ecosystems, i.e. microbial consortia, offer considerable advantages in degrading complex organic waste, to yield biomolecules of interest. We defend our opinion that this approach is more efficient and offers enhanced potential compared to the approaches that use single strain cultures.     

页岩气开采与深地微生物的相互影响

页岩气是一种特殊的天然气聚集,以吸附或游离状态存在于页岩之中。页岩气资源储量丰富,约占全球天然气能源的三分之一,主要分布在中国、北美、俄罗斯等国家和地区。页岩气开采所使用的水力压裂技术会对深地微生物产生显著影响,在水力压裂的不同阶段,微生物群落组成存在明显差异。其中,产甲烷菌能够提高页岩气的产量,而产酸细菌会造成设备腐蚀,降低页岩气的回收效率。本文概述了页岩气的开采现状、开采过程以及微生物种群的变化和潜在影响,以期促进页岩气开采与深地微生物相互影响的研究,最终推动页岩气的绿色、高效开采。