Ecoenzyme activity ratios reveal interactive effects of nutrient inputs and UVR in a Mediterranean high-mountain lake

To understand how atmospheric dust deposition and ultraviolet radiation (UVR) can affect remote, freshwater ecosystems through changes in their microbial metabolism, it is important to have tools that allow us detecting alterations and anticipating potential shifts in the functioning of microbial communities. Ecoenzyme activities (EA) are easy to measure and their ratios can be used to assess system microbial metabolism of freshwater bodies, thus evaluating the effects of global change stressors. We carried out an in situ full factorial experiment to determine how the interaction between the addition of C and P, and UVR affect the microbial metabolism of a Mediterranean high-mountain lake. Overall, activities of five ecoenzymes involved in the degradation of C-compounds and in the acquisition of N and P revealed that, under natural conditions, the growth of heterotrophic prokaryotes was dependent on organic compounds released by algae, which is consistent with a higher constraint of bacterial carbon production by C than by P or N, as suggested by EA ratios. Accordingly, the addition of a labile C source did not lead to any significant response of microbial communities, but the addition of P provoked a clear change in the microbial metabolism of the lake, promoting the growth of phytoplankton and leading heterotrophic prokaryotes to be more constrained by P, and to a lesser extent by N, in relation to C. UVR played a secondary role, probably because microbial communities inhabiting high-mountain lakes possess several evolutionary adaptations to high UVR levels. Changes in the microbial metabolism of our model lake under different scenarios of nutrient inputs and UVR can therefore be evaluated by EA ratios.     

Factors influencing capacitance-based monitoring of microbial growth.

Microbiological impedance devices are routinely used by food and manufacturing industries, and public health agencies to measure microbiological growth. Factors contributing to increases and decreases in capacitance at the culture medium-electrode interface are poorly understood. To objectively evaluate the effects of temperature, cell density and medium conductivity on capacitance, admittance values from an impedance device were standardized; capacitance was converted to susceptance to allow unit comparisons with conductance. Although increases in temperature increased susceptance, a linear relationship could not be established between the change of susceptance with temperature and conductance of the medium. Cell density by itself had no measureable effect on susceptance or conductance, indicating that cells did not impede the movement of ions in the medium or around the electrode. In a low conductivity medium, increases in conductance by the addition of ions resulted in a concomitant increase of susceptance values. However, in a high conductivity medium, increases in conductance resulted in little or no increase of susceptance values because ions saturated the electrode surface. Susceptance increased when Escherichia coli, Pseudomonas aeruginosa, Alcaligenes faecalis and Staphylococcus aureus were grown in high conductivity media because protons produced by metabolically active bacteria balance more charge on the electrode than other ions. Increases in susceptance due to bacterial growth and metabolism in low conductivity media were attributed to both increases in protons and ionic metabolites. These results indicate that capacitance may provide a better measure of microbial growth and metabolism than conductance.     

Controlling the feed rate of propanol to optimize erythromycin fermentation by on-line capacitance and oxygen uptake rate measurement

The aim of the present study was to optimize the feeding proportion of glucose and propanol for erythromycin biosynthesis by real-time monitoring and exploring its limited ratio by the on-line multi-frequency permittivity measurement. It was found that the capacitance values were sensitive to the variation of biomass concentration and microbial morphology as well as the true state of cell growth. It was most favorable to both cell growth and secondary metabolism to keep the ratio of glucose to propanol at 4.3 (g/g). The specific growth rate calculated by the capacitance measurement correctly and accurately reflected the cell physiological state. An appropriate feed rate of propanol was crucial for cell growth and secondary metabolism, as well as to improve the quality of erythromycin-A. In addition, the erythromycin production titer (10,950 U/mL) was further enhanced by 4 % when the propanol feed was regulated by step-down strategy based on both OUR (oxygen uptake rate) and the on-line monitoring capacitance.     

The mechanism of reduction in waterlogged paddy soil

Elucidation of the laws governing the reduction process in flooded rice paddy soil is indispensable for developing the lowland rice cultivation system by which the oxidation-reduction conditions for optimum growth can be maintained throughout the growth of the crop. The authors’ efforts have been focussed on the microbial metabolism of the reduction process in paddy soil, using waterlogged soil incubated in closed syringes as a simplified model of rice paddy field soil under flooded conditions. Such conditions can be assumed to occur throughout the plowed layer of field soil under flooding, except for the uppermost layer to which oxygen is supplied. One may conclude from the results of this investigation that the type of microbial metabolism in waterlogged soil changes successively according to the oxidation-reduction state from aerobic respiration in the presence of molecular oxygen, which is the most efficient energy-yielding reaction, to methane fermentation, which appears to be a less efficient energy-yielding reaction.     

氨基酸对青稞酒酿造微生物群落演替及风味代谢的驱动

【背景】环境因素是微生物生长代谢的重要驱动因素,因此,解析其对白酒酿造过程中微生物群落演替的影响对青稞酒的可控化生产具有重要作用。氨基酸作为微生物生长代谢的重要营养底物以及环境因素,其对微生物群落演替的作用尚不明确。【目的】揭示环境因素对青稞酒发酵过程中微生物群落演替及风味代谢的驱动作用。【方法】通过气相色谱-质谱联用技术对比检测肚里黄和瓦蓝两种青稞原料酿造青稞酒过程中风味物质变化情况;采用高通量扩增子测序及多元统计分析比较两种青稞酒醅中微生物群落结构特征;结合蒙特卡洛置换检验确定环境因素对微生物的影响;通过模拟发酵对以上研究结果进行验证。【结果】肚里黄青稞酒醅中酯类化合物的含量及其发酵后期乳酸杆菌相对丰度和氨基酸含量显著低于瓦蓝酒醅(P<0.05);通过生物信息学分析发现,环境因素中游离氨基酸是青稞酒发酵过程微生物群落演替重要的推动因素,且乳酸杆菌相对丰度与游离氨基酸呈显著相关;模拟发酵实验证实了特定氨基酸不足会影响乳酸杆菌生长。【结论】揭示了青稞酒发酵过程中游离氨基酸对微生物群落组装的驱动作用,进而影响青稞酒的风味品质,为青稞酒的可控发酵提供理论基础。     

Growth kinetics for shelf-life prediction: Theory and practice

Summary Predictive microbiology can be used to determine and predict the shelf-life of perishable foods under commercial distribution conditions based on microbial growth kinetics. This paper presents general microbial growth kinetics with the Monod model and the Gompertz function. Additional models are given to describe effects of food composition (e. g.a _w) and environmental conditions (e.g. temperature, gas atmosphere) as well as their interaction on the growth kinetic parameters (lag time and specific growth rate). These models can be used to predict the time to reach a critical level under any constant conditions within the range tested. A combination of microbial kinetics with an engineering accumulation approach can be used to predict the final microbial level in a food, or the loss of shelf-life, for any known time-temperature sequence, if there is no history effect or the history effect is negligible. A time-temperature indicator, could be used for predicting the remaining shelf-life of perishable foods under any distribution condition based on microbial growth kinetics.Mention of brand or firm names does not constitute an endorsement by the US Department of Agriculture over others of a similar nature not mentioned.     

Constrained proteome allocation affects coexistence in models of competitive microbial communities

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the structure and composition of microbial communities are intertwined with the metabolism of the species that inhabit them, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work, we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how proteome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show with a simple experiment that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. Then, we study our consumer-proteome-resource model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.Subject terms: Biodiversity, Microbial ecology, Microbial ecology, Bacterial physiology     

Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient

The ability of microbial species to consume compounds found in the environment to generate commercially-valuable products has long been exploited by humanity. The untapped, staggering diversity of microbial organisms offers a wealth of potential resources for tackling medical, environmental, and energy challenges. Understanding microbial metabolism will be crucial to many of these potential applications. Thermodynamically-feasible metabolic reconstructions can be used, under some conditions, to predict the growth rate of certain microbes using constraint-based methods. While these reconstructions are powerful, they are still cumbersome to build and, because of the complexity of metabolic networks, it is hard for researchers to gain from these reconstructions an understanding of why a certain nutrient yields a given growth rate for a given microbe. Here, we present a simple model of biomass production that accurately reproduces the predictions of thermodynamically-feasible metabolic reconstructions. Our model makes use of only: i) a nutrient''s structure and function, ii) the presence of a small number of enzymes in the organism, and iii) the carbon flow in pathways that catabolize nutrients. When applied to test organisms, our model allows us to predict whether a nutrient can be a carbon source with an accuracy of about 90% with respect to in silico experiments. In addition, our model provides excellent predictions of whether a medium will produce more or less growth than another () and good predictions of the actual value of the in silico biomass production.     

In Silico Geobacter sulfurreducens Metabolism and Its Representation in Reactive Transport Models

Microbial activity governs elemental cycling and the transformation of many anthropogenic substances in aqueous environments. Through the development of a dynamic cell model of the well-characterized, versatile, and abundant Geobacter sulfurreducens, we showed that a kinetic representation of key components of cell metabolism matched microbial growth dynamics observed in chemostat experiments under various environmental conditions and led to results similar to those from a comprehensive flux balance model. Coupling the kinetic cell model to its environment by expressing substrate uptake rates depending on intra- and extracellular substrate concentrations, two-dimensional reactive transport simulations of an aquifer were performed. They illustrated that a proper representation of growth efficiency as a function of substrate availability is a determining factor for the spatial distribution of microbial populations in a porous medium. It was shown that simplified model representations of microbial dynamics in the subsurface that only depended on extracellular conditions could be derived by properly parameterizing emerging properties of the kinetic cell model.     

Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing

Central carbon metabolism is highly conserved across microbial species, but can catalyze very different pathways depending on the organism and their ecological niche. Here, we study the dynamic reorganization of central metabolism after switches between the two major opposing pathway configurations of central carbon metabolism, glycolysis, and gluconeogenesis in Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida. We combined growth dynamics and dynamic changes in intracellular metabolite levels with a coarse‐grained model that integrates fluxes, regulation, protein synthesis, and growth and uncovered fundamental limitations of the regulatory network: After nutrient shifts, metabolite concentrations collapse to their equilibrium, rendering the cell unable to sense which direction the flux is supposed to flow through the metabolic network. The cell can partially alleviate this by picking a preferred direction of regulation at the expense of increasing lag times in the opposite direction. Moreover, decreasing both lag times simultaneously comes at the cost of reduced growth rate or higher futile cycling between metabolic enzymes. These three trade‐offs can explain why microorganisms specialize for either glycolytic or gluconeogenic substrates and can help elucidate the complex growth patterns exhibited by different microbial species.     

Impedance microbiology: quantification of bacterial content in milk by means of capacitance growth curves

The impedancimetric method is a technique for the rapid evaluation of milk bacterial content and also of its subproducts. Several authors have made use of culture conductance changes during bacterial growth for quantitative and qualitative assessments of microbial growth. However, interface capacitance curves, Ci, have not been used. In this paper, we quantify bacteria in cow raw milk by following their growth as the above-mentioned capacitance change time course event. With it, bigger growth variations, shorter detection times and a better coefficient of correlation with the plate count method were obtained than those yielded by conductance curves. Calibration was performed by plotting initial known concentrations, IC (CFU/ml), as a function of the time detection theshold (TDT).     

A thermodynamic theory of microbial growth

Our ability to model the growth of microbes only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. In particular, the link between energy balances and growth dynamics is still not understood. Here we demonstrate a microbial growth equation relying on an explicit theoretical ground sustained by Boltzmann statistics, thus establishing a relationship between microbial growth rate and available energy. The validity of our equation was then questioned by analyzing the microbial isotopic fractionation phenomenon, which can be viewed as a kinetic consequence of the differences in energy contents of isotopic isomers used for growth. We illustrate how the associated theoretical predictions are actually consistent with recent experimental evidences. Our work links microbial population dynamics to the thermodynamic driving forces of the ecosystem, which opens the door to many biotechnological and ecological developments.     

微重力诱变大肠杆菌快速生长突变株特性

利用旋转培养装置处理大肠杆菌,筛选生长曲线发生变化、提前进入对数期的突变菌株,对菌株进行基因芯片的表达谱分析和质谱分析,研究微重力条件下微生物的生理代谢变化和对微重力条件的适应机制。结果发现突变菌株有114个差异表达基因,其中99个基因表达上调。表达上调基因主要集中在ABC转运系统、糖代谢、三羧酸代谢、磷酸转移酶系统、核酸代谢、脂类代谢等方面。质谱分析从蛋白水平上验证了这个结果。表明经过微重力处理可以筛选到生长加快的菌株,生长加快是菌株相关代谢水平上调的结果。空间微重力通过对微生物生长代谢相关基因的影响来使菌株适应空间环境。     

Controlled gas environments in industrial fermentations

The gas environment is of major importance in controlling aerobic fermentation processes for the manufacture of microbial products. Oxygen and carbon dioxide levels in gas-liquid equilibria affect productivity and energy consumption in such processes and appear to be implicated in the regulation of microbial metabolism. Gas-liquid transfer has been intensively studied by many investigators for Newtonian and non-Newtonian fluids, primarily in terms of oxygen-limitation in biomass and product formation. More recentreports show that microbial growth and product formation are affected by levels of oxygen and carbon dioxide in the gas environment, suggesting that microbial metabolism may be directed towards specific products by the control of such environments. High product concentrations may also be obtained by solid substrate fermentations with mycelial organisms cultured on semi-solid agricultural products at low moisture contents. Such methods are commonly used in the Orient for the manufacture of enzymes and traditional fermented foods and could probably be extended to other microbial products. This review covers fundamental aspects of engineering research in microbial processes that suggest applications for controlled gas environments in submerged culture and solid substrate fermentations of potential industrial interest.     

Bacillus spp.的筛选鉴定及浸矿渣效果研究

目的:研究Bacillus spp.的生长特性及浸镉渣效果。方法:采用9K培养基划线分离纯化目标菌种,利用传统的测定方法测定其生长特征,采用16S rDNA对菌株进行分子生物学鉴定,最后对该菌株浸三种矿渣浸出效果进行了分析。结果:该微生物形态为扁球形,革兰氏染色呈阳性,能运动,单生鞭毛;最适生长温度30℃,最适pH值为3;代谢类型为兼性营养型;耐受NaCl浓度为4%;微生物氧化酶为阴性,接触酶为阳性;经鉴定该菌株属于Bacillus属。以5%的接种量,培养基pH为3条件下,镉浸出效果较好,沉渣中浸出率为90.4%,其余两种渣中浸出效果最佳。结论:Bacillus spp.可应用于镉渣中镉的浸出。     

基因组规模代谢网络模型构建及其应用

微生物制造产业的发展迫切需要进一步提高认识、设计和改造微生物细胞代谢的能力,以推动工业生物技术快速发展。随着微生物全基因组序列等高通量数据的不断积聚和生物信息学策略的持续涌现,使全局性、系统化地解析、设计、调控微生物生理代谢功能成为可能。而基于基因组序列注释和详细生化信息整合的基因组规模代谢网络模型(GSMM)构建为全局理解和理性调控微生物生理代谢功能提供了最佳平台。以下在详述GSMM的应用基础上,描述了如何构建一个高精确度的GSMM,并展望了未来的发展方向。     

Measurement of fungi by an indirect conductimetric assay

AIMS: To investigate the growth of fungi using an indirect conductimetric assay and derive, experimentally and theoretically, the relationship between microbial concentration and electrical conductivity change. METHODS AND RESULTS: The indirect assay, in which change in electrical conductivity of an alkaline solution (NaOH) is produced by absorption of CO2 from microbial metabolism, was conducted with the Bactometer (bioMerieux, Marcy-l'Etoile, France) for the enumeration of fungi. A linear relationship was obtained between detection time and logarithmic initial microbial concentration. This indirect assay used growth media, which could not be used in the direct conductimetric assay, to monitor fungal growth. CONCLUSIONS: The indirect assay does not depend on the growth media and the turbidity of sample and could offer a simple and rapid assay for the measurement of fungal growth under various conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: The indirect assay is applicable for rapid detection of fungi, estimation of the growth rate and evaluation of antifungal activity.     

Closure effects on oxygen transfer and aerobic growth in shake flasks

Oxygen mass transfer in shake flasks is an important aspect limiting the culture of aerobic microorganisms. In this work, mass transfer of oxygen through a closure and headspace of shake flasks is investigated. New equations for prediction of kGa in shake flasks with closures are introduced. Using Pseudomonas putida, microbial growth on glucose (fast metabolism) and phenol (slow metabolism) in shake flasks with closures were studied, considering both substrate and oxygen restrictions. A combined model for oxygen mass transfer and microbial growth is shown to accurately predict experimental oxygen concentrations and oxygen yield factors during growth experiments more accurately than previous models.     

Endophytic microorganisms—promising applications in bioremediation of greenhouse gases

Bioremediation is a technique that uses microbial metabolism to remove pollutants. Various techniques and strategies of bioremediation (e.g., phytoremediation enhanced by endophytic microorganisms, rhizoremediation) can mainly be used to remove hazardous waste from the biosphere. During the last decade, this specific technique has emerged as a potential cleanup tool only for metal pollutants. This situation has changed recently as a possibility has appeared for bioremediation of other pollutants, for instance, volatile organic compounds, crude oils, and radionuclides. The mechanisms of bioremediation depend on the mobility, solubility, degradability, and bioavailability of contaminants. Biodegradation of pollutions is associated with microbial growth and metabolism, i.e., factors that have an impact on the process. Moreover, these factors have a great influence on degradation. As a result, recognition of natural microbial processes is indispensable for understanding the mechanisms of effective bioremediation. In this review, we have emphasized the occurrence of endophytic microorganisms and colonization of plants by endophytes. In addition, the role of enhanced bioremediation by endophytic bacteria and especially of phytoremediation is presented.