Near infrared spectroscopy for bioprocess monitoring and control: current status and future trends

The development of Near Infrared Spectroscopy has paralleled that of the PC, and the application of NIR in many industries has undergone explosive growth in recent years. This has been particularly apparent in the area of microbial and cell culture system monitoring and control. Potentially, NIR offers the prospect of real-time control of the physiology of cultured cells in fermenters, leading to marked improvements in authenticity, purity and production efficiency. Despite this, NIR is not yet as widely applied within the bioprocessing industry as its potential might suggest. This review critically evaluates the development of this rapidly moving area as it pertains to microbial and cell culture system control and highlights the critical stages in the development of the technology. It indicates the work that must still be carried out if the full potential of NIR is to be exploited in making proteins, hormones and antibiotics by the fermentation route. The review comes at a particularly timely moment when NIR stands on the threshold of widespread acceptance in bioprocessing. This is the ideal moment to assess what the technology can offer the microbiologist, and where it may develop in the future.     

害虫微生物防治的目标体系与效益评价方法

害虫微生物防治系统是复杂的多目标复合生态系统．对系统进行多目标效益评价有助于了解系统现状,遴选最佳防治技术,根据害虫防治的一般要求,结合微生物防治的有关特点,建立了害虫微生物防治的目标体系．对基于估计相对位置的方案排队法和混合优序图法分别进行改进,用改进算法对系统进行效益评价和方案择优,给出了计算软件．同时指出,在生态系统的评价管理中,多目标决策方法是科学合理、行之有效的定量工具．     

``BACWAVE,' a Spatial–Temporal Model for Traveling Waves of Bacterial Populations in Response to a Moving Carbon Source in Soil

Abstract Previously, we discovered the phenomenon of wavelike spatial distributions of bacterial populations and total organic carbon (TOC) along wheat roots. We hypothesized that the principal mechanism underlying this phenomenon is a cycle of growth, death, autolysis, and regrowth of bacteria in response to a moving substrate source (root tip). The aims of this research were (i) to create a simulation model describing wavelike patterns of microbial populations in the rhizosphere, and (ii) to investigate by simulation the conditions leading to these patterns. After transformation of observed spatial data to presumed temporal data based on root growth rates, a simulation model was constructed with the Runge–Kutta integration method to simulate the dynamics of colony-forming bacterial biomass, with growth and death rates depending on substrate content so that the rate curves crossed over at a substrate concentration within the range of substrate availability in the model. This model was named ``BACWAVE,' standing for ``bacterial waves.' Cyclic dynamics of bacteria were generated by the model that were translated into traveling spatial waves along a moving nutrient source. Parameter values were estimated from calculated initial substrate concentrations and observed microbial distributions along wheat roots by an iterative optimization method. The kinetic parameter estimates fell in the range of values reported in the literature. Calculated microbial biomass values produced spatial fluctuations similar to those obtained for experimental biomass data derived from colony forming units. Concentrations of readily utilizable substrate calculated from biomass dynamics did not mimic measured concentrations of TOC, which consist not only of substrate but also various polymers and humic acids. In conclusion, a moving pulse of nutrients resulting in cycles of growth and death of microorganisms can indeed explain the observed phenomenon of moving microbial waves along roots. This is the first report of wavelike dynamics of microorganisms in soil along a root resulting from the interaction of a single organism group with its substrate. Received: 2 October 1999; Accepted: 9 March 2000; Online Publication: 28 August 2000     

UASB反应器中影响污泥颗粒化的工程因素

研究了具有不同微生物群系的接种污泥、流动方式和流速对上流式厌氧污泥床(UASB)反应器中活性污泥粒化的影响。颗粒化过程包括：微生物絮凝体的形成、亚核的形成,亚核增长和颗粒成熟四个阶段。微絮凝体的形成取决于酸化菌的作用。流体的动量传递和流体对悬浮物的剪切作用是影响亚核形成的关键性工程因素。为此提出最低流速概念,即形成污泥膨胀床的最低流速。合适的进料速率、污泥负荷、布水均匀性以及碱度控制是UASB反应器工程放大和过程控制的四大要素。     

A system for photographing cell-sized particles moving at high velocities

A system is described that was used to photograph 3.9 micron diameter DNA-coated beads traveling at speeds up to 30,000 cm/s. The resolution of the optics is 1 micron, so smaller particles moving more slowly could also be photographed. A useful feature is the 15 cm working distance between the optical components and the object to be photographed. Some alternative applications for this type of equipment include studies of cell behavior in turbulence, microbial disruption processes, and membrane poration techniques.     

营养相互作用对传统发酵食品微生物群落构建的推动作用研究进展

传统发酵食品是由自然接种的多微生物组成的混菌体系,了解微生物群落自发式构建的机制是认识发酵机理和调控发酵的关键。尽管大量的测序数据已经对传统发酵食品中微生物群落的结构和功能有了较为清晰的认识,但是仍然不清楚微生物群落自发式构建的机制。本文提出微生物群落是分布式的代谢系统,微生物之间的营养相互作用推动了传统发酵食品微生物群落的自发式构建。本文主要阐述了营养相互作用的概念、发生的机理以及研究方法体系,整理了传统发酵食品中微生物之间营养相互作用的研究进展,并提出了未来的研究方向。通过营养相互作用推动的传统发酵食品微生物群落的自发式构建有助于定向控制发酵过程中的微生物种类、提高生产效率和改善发酵质量。     

Maximization of steady-state bacterial production in a chemostat with pH and substrate control.

This analytical study deals with the steady-state behavior and control of microbial growth in continuous cultures. A second order Haldane-Monod model of continuous cultures is used as a basis for study of the effects of the adjustment of pH by the addition of acidic (or basic) materials. The treatment of a hydrogen ion concentration, in addition to substrate and microbial concentrations as state variables, results in a third order system of equations describing the process. The analysis of the system in equilibrium yields several admissible steady states, that is, steady states which satisfy all constraints. An optimal control problem is formulated and subsequently solved to maximize steady-state microbial production.     

Comparison of different microbial biomass and activity measurement methods in metal-contaminated soils

The aims of this study were: (1) to compare different microbial methods of detecting the effects of heavy metals on the functioning of the soil ecosystem; and (2) to evaluate the effect of incubation on microbial biomass and microbial activity in soils that were not pre-incubated after sampling in order to determine their suitability for measuring the effects of heavy metals on the soil microbial ecosystem. The microbial biomass methods (included: biomass C, N and ninhydrin-N by fumigation-extraction (FE); substrate-induced respiration (SIR); soil ATP content and microbial activity as evolved CO2-C and arginine ammonification. All were tested in soils from the Woburn Market Garden Experiment. Due to past sludge application the soils contained, Zn, Cu or Ni at around current European Union upper limits and Cd at up to three times the limit. The amount of microbial biomass in metal-contaminated soils was about half of that found in soils from the experiment that received uncontaminated organic manure or inorganic fertilizer. The amount of biomass measured by FE and soil ATP content in incubated soils showed little change over 20 days incubation. However, SIR measurements were statistically affected over the first few days of incubation. The rates of arginine ammonification were higher in this order: farmyard manure (FYM)>inorganic fertilizer>sewage-sludge throughout the incubation. However, the evolved CO2-C rates were not significantly different among the treatments. Discriminant analysis confirmed smaller amounts of biomass in the metal-contaminated soils than in the other treatments. Linked properties, such as relationships between biomass and soil organic matter, or biomass-specific respiration rates, may provide "internal control" which may help overcome problems of establishing suitable control, or comparative measurements, when moving from experimental to natural environments.     

群体感应与微生物耐药性

微生物耐药性已成为全球关注的严重问题,其演化机制和调控机理也已成为研究热点。近年来的研究发现,一些微生物耐药性机制受到群体感应系统的调控。群体感应是一种在微生物界广泛存在并与菌体密度关联的细胞-细胞间的通讯系统。高密度的菌落群体能够产生足够数量的小分子信号,激活下游包括致病毒力和耐药性机制在内的多种细胞进程,耐受抗生素并且危害寄主。本文结合国内外最新的研究进展,对微生物群体感应系统的研究现状进行了概括性介绍,重点阐述了群体感应系统对微生物耐药性机制的调控作用,如微生物生物被膜形成和药物外排泵调控等方面的作用,并探讨了利用群体淬灭控制微生物耐药性的新策略。     

Enhancement of Ca2+ release from limestone by microbial extracellular carbonic anhydrase

Three experimental systems were set up to investigate whether carbonic anhydrase (CA) from microorganisms actually plays the driving role in limestone dissolution. In one, redistilled water served as negative control. In a second, microbial origin CA enzyme solution supplemented with CA special inhibitor acetazolamide (AZ) served as positive control. A third contained a crude enzyme solution of microbial CA. The results showed that the amount of released Ca2+ from limestone in a CA non-inhibited system increased by 2.4 times compared to a CA inhibited system, and increased by 11.7 times compared to the redistilled water control. These experiments demonstrated that microbial origin CA significantly enhanced Ca2+ release from limestone (P < 0.01), and therefore, proved the significant driving effect of microbial CA on limestone dissolution. The results also suggested that microbially derived CA might exert an important influence on biokarst process.     

Characterization of microbial community in an aerobic moving bed biofilm reactor applied for simultaneous nitrification and denitrification

A continuous-flow moving bed biofilm reactor (MBBR) under aerobic conditions was established for simultaneous nitrification and denitrification (SND), and microbial communities were investigated by a combination of denaturing gel gradient electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). DGGE analysis has revealed more similar microbial community structures formed in the biofilms with more similar carbon nitrogen (C/N) ratios. FISH analysis shows that the dominance of both Betaproteobacteria ammonia-oxidizing bacteria and Nitrospira-like nitrite-oxidizing bacteria were negatively correlated to C/N ratios. Sequence analysis of DGGE bands has indicated the presence of anoxic denitrifying bacteria Agrobacterium tumefaciens and Rhizobium sp., suggesting that the oxygen gradient inside the biofilm may be responsible for the mechanism of SND in aerobic MBBRs. The study confirms that appropriate control of microbial community structure resulting from optimal C/N ratio is beneficial in improving SND, thus optimizing nitrogen removal in aerobic MBBR. The established SND-based MBBR can save operation space and time in comparison to the traditional nitrogen removal process, and might be very attractive for future practical applications.     

冬季作物对稻田土壤微生物量碳、氮和微生物熵的短期影响

研究不同的冬季作物马铃薯、黑麦草、紫云英、油菜在"冬季作物-双季稻"轮作种植制度下短期内对稻田土壤微生物碳、氮和微生物熵的影响,在湖南省土壤肥料研究所的实验网室内设置了小区试验.试验结果表明:几种冬季作物均提高了稻田土壤微生物碳、氮含量,黑麦草明显提高了土壤微生物量碳和微生物熵,紫云英明显提高了土壤微生物量氮.冬季作物对土壤微生物量碳和土壤微生物量氮的季节性影响变化趋势基本一致,紫云英、马铃薯处理的土壤微生物量C、N含量均在水稻生育期间8月中旬达到最大值.     

山竹岩黄蓍固沙群落对土壤养分及生物活性的改良效应

以半流动沙丘为对照,对5、10和22年生山竹岩黄蓍人工固沙群落不同层次(0~10、10~20和20~30cm)土壤的养分状况、微生物生物量和土壤酶活性进行了对比研究.结果表明:采用山竹岩黄蓍固定流沙后,随着群落年龄的增长,土壤中C、N、P、K含量及生物活性均明显提高.其中,0~10cm土层的增长幅度显著高于10~30cm土层.0~30cm土层中C/N由7.3增加到8.5;土壤微生物生物量碳、氮、磷含量以及土壤脲酶、磷酸单酯酶、蔗糖酶、蛋白酶、脱氢酶、硝酸还原酶和多酚氧化酶的活性均有所提高.其中,0~10cm土层中蔗糖酶的活性是对照的49.7~284.5倍.土壤微生物生物量碳、氮、磷分别与土壤有机碳、全氮、全磷以及微生物生物量与酶活性之间存在显著的正相关关系.     

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination

A 90 days greenhouse experiment was conducted for evaluation of soil microbial diversity in different treatments of rhizospheric and nonrhizospheric oil sludge contaminated soil. Various pot treatments (T1–T5) were as follows: 2% oil sludge contaminated soil was considered as control (T1); augmentation of control with preadapted microbial consortium was T2; addition of Vetiver zizanioide to control was T3; bioaugmentation of control along with V. zizanioide was T4; and bioaugmentation with V. zizanioide and bulking agent was T5. During the study, different microbial populations were determined in all treatments. Additionally, soil microbial diversity using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) of 16S rDNA was carried out. At the end of experimental period, significant increase in microbial number in bioaugmented rhizospheric treatments (T4 and T5) was observed as compared to non-rhizospheric and non-bioaugmented treatments (T2 and T3). The community and sequencing results revealed that combined treatment of plant and microbes resulted in improved microbial species and number. The dominant phyla belonged to γ proteobacteria, β proteobacteria, Chloroflexi, firmicutes, and uncultured bacteria. It is concluded that plant–microbe–soil system supports immense oil degrading microbial diversity and can be used as an effective indicator tool for remediation of oil sludge contaminated sites.     

鄱阳湖湿地土壤微生物群落结构沿地下水位梯度分异特征

为了揭示地下水位梯度对湿地土壤微生物群落的影响,在鄱阳湖典型碟形湖泊白沙湖洲滩湿地设置了200m×300m大样地,沿地下水位梯度划分4个样带(从湖岸到湖心依次为GT-A,GT-B,GT-C,GT-D),采集了不同梯度带的土壤样品,利用磷脂脂肪酸法分析其土壤微生物群落结构分异特征。结果表明,随着地下水位抬升,土壤pH和沙粒含量升高,而有机碳、容重、粘粒和粉粒含量降低。与地下水位最低的梯度(GT-A)相比,地下水位在地表上下波动(GT-D)时,土壤微生物量碳氮及其分配比例分别增加了2.82、4.30、5.77和7.15倍;土壤微生物总量、细菌生物量、放线菌生物量、革兰氏阳性细菌及革兰氏阴性细菌生物量分别增长了106.8%、117.2%、74.9%,107.9%和207.2%。洲滩地下水位梯度的升高增加了土壤微生物群落的环境压力,进而降低了其群落结构的多样性。土壤微生物群落结构组成与土壤pH、含水量、沙粒含量以及碳氮比呈显著相关关系,而土壤微生物商则主要受pH和土壤质地的影响。以上结果表明地下水位梯度所引起的土壤微环境变化对微生物量、土壤有机碳周转和群落结构均产生了深刻影响。     

How do we make indoor environments and healthcare settings healthier?

It is now well accepted that our modern lifestyle has certain implications for our health (Schaub et al., 2006 ), mainly as a result of our willingness to remove ourselves from the biological diversity of our natural environments (Roduit et al., 2016 ), while still being drawn inextricably to interact with it (Kellert and Wilson, 1995 ). Much of our interaction with the biological world is shaped by our interaction with the microbiological world. The bacteria, fungi, viruses, archaea and protists that comprise the microbiome of this planet, are also key to the development and normal functioning of our bodies. Our immune system is built to shepherd our microbial exposure, ensuring that microbial organisms that we need are kept close (but not too close), and that less‐desirable organisms are expelled or killed before they can do too much damage. By moving from a life interacting with nature on a regular basis, to a life in which we isolate ourselves physically from natural microbial exposure, we may have instigated one of the great plagues of the 21st century; chronic immune disorders.     

Spatial variability of soil nutrients and microbiological properties after the establishment of leguminous shrub Caragana microphylla Lam. plantation on sand dune in the Horqin Sandy Land of Northeast China

The objective of this study is to determine the spatial variability of nutrients, microbial biomass, and enzyme activities of soil due to the establishment of shrub plantation on moving sandy dunes, as part of an effort to understand the microenvironmental factors that control the soil microbiological properties. Caragana microphylla Lam., an indigenous leguminous shrub, is the dominant plant species used to control desertification in the semi-arid Horqin Sandy Land of Northeast China. In a 26-year-old C. microphylla plantation, soil samples were collected from three soil depths (0-5 cm, 5-10 cm, and 10-20 cm), three slope positions (windward slope, top slope, and leeward slope), and two microsites (under shrubs and between shrubs). The results showed significant differences in soil EC, nutrient content (except for total K), microbial biomass C and N, and the activities of dehydrogenase, urease, and protease at different slopes, soil depths, and microsites. Significant differences in pH at different microsites and slopes, soil moisture and polyphenol oxidase activity at different soil depths and slopes, and activities of phosphomonoesterase and nitrate reductase at different soil depths were also observed. The soil nutrient contents and microbiological activities were greater in the surface soil layer and decreased with the increase of soil depth. Soil organic C, total N, total P, available P and K, microbial biomass C and N, and the activities of enzymes tested (except for protease) under shrubs were higher than those in between shrubs. Furthermore, significant correlations among soil organic C, microbial biomass C and N, the activities of phosphomonoesterase, dehydrogenase, urease, protease, and nitrate reductase were observed, and correlations were also found among EC, total N, total P, available P and K, enzyme (except for polyphenol oxidase) activities, and microbial biomass C and N contents. These results suggest that microenvironmental factors (slope, soil depth and microsite) have significant influences on the spatial distribution of soil nutrients and microbiological properties when the C. microphylla sand-fixing plantation is established in the moving sand dunes in the Horqin Sandy Land.     

Visual control of prey-capture flight in dragonflies

Interacting with a moving object poses a computational problem for an animal's nervous system. This problem has been elegantly solved by the dragonfly, a formidable visual predator on flying insects. The dragonfly computes an interception flight trajectory and steers to maintain it during its prey-pursuit flight. This review summarizes current knowledge about pursuit behavior and neurons thought to control interception in the dragonfly. When understood, this system has the potential for explaining how a small group of neurons can control complex interactions with moving objects.     

视动震颤(OKN)眼动控制系统中的颜色通道

用亮度相等的不同颜色构成的等亮度彩色运动条纹(Isoluminant chromatic moving gratings)来进行OKN眼动跟踪实验,探讨它是否与由亮度差别构成的黑白运动条纹图象一样引起OKN反应。实验结果表明在等亮度彩色运动条纹图象(没有亮度差别只有颜色差别)刺激下,视动系统可产生与黑白运动条纹刺激下同样的OKN反应,并且与各单原色运动条纹刺激下的OKN反应也一致。说明0KN眼动跟踪中的运动检测存在颜色通道。本文并提出了一种基于颜色的运动检测模型。