Artificial microbial consortia for bioproduction processes

The application of artificial microbial consortia for biotechnological production processes is an emerging field in research as it offers great potential for the improvement of established as well as the development of novel processes. In this review, we summarize recent highlights in the usage of various microbial consortia for the production of, for example, platform chemicals, biofuels, or pharmaceutical compounds. It aims to demonstrate the great potential of co-cultures by employing different organisms and interaction mechanisms and exploiting their respective advantages. Bacteria and yeasts often offer a broad spectrum of possible products, fungi enable the utilization of complex lignocellulosic substrates via enzyme secretion and hydrolysis, and microalgae can feature their abilities to fixate CO₂ through photosynthesis for other organisms as well as to form lipids as potential fuelstocks. However, the complexity of interactions between microbes require methods for observing population dynamics within the process and modern approaches such as modeling or automation for process development. After shortly discussing these interaction mechanisms, we aim to present a broad variety of successfully established co-culture processes to display the potential of artificial microbial consortia for the production of biotechnological products.     

Heterotrophic dinitrogen fixation (acetylene reduction) in phosphate-fertilised Microcoleus chthonoplastes microbial mat from the hypersaline inland lake ‘la Salada de Chiprana’ (NE Spain)

Microcoleus chthonoplastes dominated microbial mats are conspicuous along the shallow littoral zone in Lake Chiprana, a hypersaline lake located in the Ebro river basin in north-eastern Spain. Pigment data show that these mats included diatom species and anoxygenic phototrophs, Chloroflexus-type bacteria and purple bacteria. In situ, these mats showed low rates of dinitrogen fixation (acetylene reduction). Acetylene reduction was stimulated about 30-fold in excised mats after moderate phosphate fertilisation during 2 weeks incubation in a mesocosm. Pigment analyses showed that this treatment had little impact on the phototrophic community structure, except that it induced a decrease of Chloroflexus-type bacteria. The use of metabolic inhibitors indicated that methanogenic archaea and aerobic heterotrophic bacteria were the major dinitrogen fixers in this system. This is in agreement with the fact that the mat-building cyanobacterium M. chthonoplastes lacks the dinitrogenase reductase nifH gene and with the fact that acetylene reduction rates were strongly stimulated by additions of H₂/CO₂, methanol, fructose and sucrose, but not by lactate, acetate, formate and glucose. No significant differences where found for acetylene reduction rates when comparing light and dark incubations of these microbial mats. However, acetylene reduction rates were enhanced in the light when the near infrared (NIR) light was filtered out, which arrested anoxygenic photosynthesis. We suggest, therefore, that the chemoheterotrophic dinitrogen fixing bacteria were in competition with anoxygenic phototrophic bacteria for organic substrates, while the latter did not contribute to dinitrogen fixation in the mat.     

Modelling the Cell Cycle and Cell Movement in Multicellular Tumour Spheroids

This paper analyses a recent mathematical model of avascular tumour spheroid growth which accounts for both cell cycle dynamics and chemotactic driven cell movement. The model considers cells to exist in one of two compartments: proliferating and quiescent, as well as accounting for necrosis and apoptosis. One particular focus of this paper is the behaviour created when proliferating and quiescent cells have different chemotactic responses to an extracellular nutrient supply. Two very different steady-state behaviours are identified corresponding to those cases where proliferating cells move either more quickly or more slowly than quiescent cells in response to a gradient in the extracellular nutrient supply. The case where proliferating cells move more rapidly leads to the commonly accepted spheroid structure of a thin layer of proliferating cells surrounding an inner quiescent core. In the case where proliferating cells move more slowly than quiescent cells the model predicts an interesting structure of a thin layer of quiescent cells surrounding an inner core of proliferating and quiescent cells. The sensitivity of this tumour structure to the cell cycle model parameters is also discussed. In particular variations in the steady-state size of the tumour and the types of transient behaviour are explored. The model reveals interesting transient behaviour with sharply delineated regions of proliferating and quiescent cells.     

Cooperative differentiation through clustering in multicellular populations

The coordinated development of multicellular organisms is driven by intercellular communication. Differentiation into diverse cell types is usually associated with the existence of distinct attractors of gene regulatory networks, but how these attractors emerge from cell-cell coupling is still an open question. In order to understand and characterize the mechanisms through which coexisting attractors arise in multicellular systems, here we systematically investigate the dynamical behavior of a population of synthetic genetic oscillators coupled by chemical means. Using bifurcation analysis and numerical simulations, we identify various attractors and attempt to deduce from these findings a way to predict the organized collective behavior of growing populations. Our results show that dynamical clustering is a generic property of multicellular systems. We argue that such clustering might provide a basis for functional differentiation and variability in biological systems.     

A Computational Model for Cortical Endosteal Surface Remodeling Induced by Mechanical Disuse

In mechanical disuse conditions associated with immobilization and microgravity in spaceflight, cortical endosteal surface moved outward with periosteal surface moving slightly or unchanged, resulting in reduction of cortical thickness. Reduced thickness of the shaft cortex of long bone can be considered as an independent predictor of fractures. Accordingly, it is important to study the remodeling process at cortical endosteal surface. This paper presents a computer simulation of cortical endosteal remodeling induced by mechanical disuse at the Basic Multicellular Units level with cortical thickness as controlling variables. The remodeling analysis was performed on a representative rectangular slice of the cross section of cortical bone volume. The pQCT data showing the relationship between the duration of paralysis and bone structure of spinal cord injured patients by Eser et al. (2004) were used as an example of mechanical disuse to validate the model. Cortical thickness, BMU activation frequency, mechanical load and principal compressive strain for tibia and femur cortical models were simulated. The effects of varying the mechanical load and maximum BMU activation frequency were also investigated. The cortical thicknesses of femur and tibia models were both consistent with the clinical data. Varying the decreasing coefficient in mechanical load equation had little effect on the steady state values of cortical thickness and BMU activation frequency. However, it had much effect on the time to reach steady state. The maximum BMU activation frequency had effects on both the steady state value and the time to reach steady state for cortical thickness and BMU activation frequency. The computational model for cortical endosteal surface remodeling developed in this paper can be further used to quantify and predict the effects of mechanical factors and biological factors on cortical thickness and help us to better understand the relationship between bone morphology and mechanical as well as biological environment.     

Synergistic effect of Pseudomonas putida and Bacillus amyloliquefaciens ameliorates drought stress in chickpea (Cicer arietinum L.)

Two plant growth promoting rhizobacteria (PGPR) Pseudomonas putida NBRIRA and Bacillus amyloliquefaciens NBRISN13 with ability to tolerate abiotic stress along with multiple PGP traits like ACC deaminase activity, minerals solubilisation, hormones production, biofilm formation, siderophore activity were evaluated for their synergistic effect to ameliorate drought stress in chickpea. Earlier we have reported both the strains individually for their PGP attributes and stress amelioration in host plants. The present study explains in detail the possibilities and benefits of utilizing these 2 PGPR in consortium for improving the chickpea growth under control and drought stressed condition. In vitro results clearly demonstrate that both the PGPR strains are compatible to each other and their synergistic growth enhances the PGP attributes. Greenhouse experiments were conducted to evaluate the effect of inoculation of both strains individually and consortia in drought tolerant and sensitive cultivars (BG362 and P1003). The growth parameters were observed significantly higher in consortium as compared to individual PGPR. Colonization of both PGPR in chickpea rhizosphere has been visualized by using gfp labeling. Apart from growth parameters, defense enzymes, soil enzymes and microbial diversity were significantly modulated in individually PGPR and in consortia inoculated plants. Negative effects of drought stress has been ameliorated and apparently seen by higher biomass and reversal of stress indicators in chickpea cultivars treated with PGPR individually or in consortia. Findings from the present study demonstrate that synergistic application has better potential to improve plant growth promotion under drought stress conditions.     

Enhanced decolorization of sulfonated azo dye methyl orange by single and mixed bacterial strains AK1, AK2 and VKY1

Abstract

Methyl orange, a sulfonated azo dye having various industrial applications was decolorized by three bacteria Bacillus sp. strain AK1, Lysinibacillus sp. strain AK2 and Kerstersia sp. strain VKY1. The effect of various factors such as dye concentration, pH, temperature and NaCl concentration on decolorization was investigated. At 200?mg/L methyl orange concentration, the strains AK1, AK2 and VKY1 exhibited maximum decolorizing potential of 93, 95 and 96%, respectively, at temperature 35?°C and pH 7.0 within 18?h of incubation. These strains decolorized the dye over a wide range of pH (5–10), temperature (15–55?°C), and NaCl concentration (5–20?g/L). Further, these strains decolorize up to 800?mg/L concentrations of methyl orange within 24?h. The dye decolorization efficiency was further increased by using different consortia of these three strains which could decolorize the dye completely within 12?h of incubation. The cell-free extracts of the strains AK1, AK2 and VKY1 grown on methyl orange exhibited the azoreductase activity of 0.4794, 1.56 and 1.01?µM/min/mg protein, respectively. HPLC and FTIR analysis of the dye decolorized sample indicated the formation of 4-aminobenzenesulfonic acid and N,N-dimethyl-p-phenylenediamine as breakdown products of azo bond. The high decolorization potential of these bacterial strains individually and in consortia has potential application in remediation of dye effluent.     

基于代谢组的厌氧氨氧化菌群对温度的响应机制

【背景】在环境工程领域中,大多数耐冷菌从活性污泥中分离得到。了解活性污泥菌群对低温的响应有助于耐冷菌的驯化培养。【目的】以厌氧氨氧化污泥菌群作为研究对象,研究温度对厌氧氨氧化菌群代谢通路与代谢产物的影响,以期初步阐释厌氧氨氧化菌群低温响应机理。【方法】在25°C与35°C条件下驯化培养厌氧氨氧化污泥,研究温度对反应器脱氮效能、菌群活性与生长以及群落结构的影响,通过代谢组学比较两个温度下厌氧氨氧化菌群代谢物丰度以及代谢通路活性。【结果】虽然低温导致厌氧氨氧化菌群CO_2固定、TCA循环与丙酮酸代谢的下调,进而导致氮去除活性以及增长速率显著下降,但菌群RNA合成水平、腐胺与信号分子合成上调,从而通过转录调控、调控膜脂组成与改变膜结构的方式,调控菌群代谢以适应低温环境。【结论】从分子机理的角度探究了厌氧氨氧化污泥菌群适应低温环境的生理机制,首次阐释了腐胺与信号分子在污泥菌群适应低温过程中的重要作用。     

Arsenic Contamination in Agricultural Soil Reduces Metabolic Activity of Total and Free-Living Nitrogen-Fixing Bacteria as Revealed by Real-Time qPCR

Laboratory microcosms were used to assess the impact of arsenic (As) contamination on agricultural soil bacterial activity focusing free-living nitrogen fixers for three months. Periodically collected microcosm samples were analyzed by RT–qPCR following extraction of total RNA and cDNA preparation for assessing the metabolically active bacterial population. RT–qPCR data showed the gradual increase of 16S rRNA and nifH gene expression, and relative activity of diazotrophs in the enriched soil bacterial consortia under short time As exposure up to 20 ppm and 10 ppm, respectively. A similar trend of these variables was also noticed but up to 1 ppm As when incubating the bulk soil for the same duration. Reduced bacterial activity was noticed at higher concentration of As although in short time exposure. Extending the As exposure time, the bacterial activities in both enriched consortia and bulk soil were decreased. Although, the relative activity of diazotrophs in enriched consortia was increased in presence of 10 ppm As, the same was decreased in bulk soil when exposed to >1 ppm As for long time indicating susceptibility of nitrogen fixer to As contamination in soil. PCA of the data obtained also indicated a negative correlation between As concentrations and diazotrophic activity.