Microarray Applications in Microbial Ecology Research

Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.

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瘤胃微生物多样性及功能性研究方法概述

庞大的瘤胃微生物群系之间存在着共生关系,影响着宿主的代谢,是反刍动物营养学的研究热点之一.通过基于16S rRNA的分子生物学方法,如探针法、实时定量PCR法、DGGE/TGGE,RAPD和RFLP技术等研究瘤胃微生物多样性及组成结构,应用宏基因组学如建立YAC文库、BAC文库等研究方法对瘤胃微生物功能特征进行更深入的研究,实现改善反刍动物乳、肉产品品质的目的.     

Microbial Ecology: Fundamentals and Applications

Microbial Ecology:Fundamentals and Applications《微生物生态学:原理与应用》R.M.Atlas和R.Bartha著,Addison-Wesley出版公司,1981年,英文。本书比较全面系统地阐述了微生物生态学的基本知识,重点论述了微生物生态学的研究方法及其在实践上的应用。本书虽是作为大学     

对《微生物生态学原理与应用》一书的评价

1981年美国Addison-Wesley出版公司出版了一本《微生物生态学原理与应用》(Microbial Ecology:Fundamentals aud Applications)全书560页。约80万字。作者是美国肯塔基州路易斯维尔(Louisville)大学的R. M. 阿特拉斯(Ronaild M. Atlas)教授及美国新泽西州鲁特杰尔斯(Bu(?)gers)大学的R.巴尔塔(Richard Bartha)教授。他们针对美国许多大学开设的生物生态学课,但又缺乏教材的情况而写了这本教科书。全     

Production of Electricity and Butanol from Microalgal Biomass in Microbial Fuel Cells

Chlorella vulgaris (a freshwater microalga) and Dunaliella tertiolecta (a marine microalga) were grown for bulk harvest, and their biomass was tested as feedstock for electricity production in cubic two-chamber microbial fuel cells (MFCs) at 37°C. The anode inoculum was anaerobic consortium from a municipal sewage sludge digester, enriched separately for the two microalgal biomass feedstocks. After repeated subculturing of the two anaerobic enrichments, the maximum power density obtained in MFCs was higher from C. vulgaris (15.0 vs. 5.3 mW m^?2) while power generation was more sustained from D. tertiolecta (13 vs. 9.8 J g^-1 volatile solids). Anolytes of algal biomass-fed MFCs also contained substantial levels of butanol (8.7–16 mM with C. vulgaris and 2.5–7.0 mM with D. tertiolecta), which represents an additional form of utilizable energy. Carryover of salts from the marine D. tertiolecta biomass slurry resulted in gradual precipitation of Ca and Mg phosphates on the cathode side of the MFC. Polymerase chain reaction-denaturing gradient gel electrophoresis profiling and sequencing of bacterial communities demonstrated the presence of Wolinella succinogenes and Bacteroides and Synergistes spp. as well as numerous unknown bacteria in both enrichments. The D. tertiolecta enriched consortium contained also Geovibrio thiophilus and Desulfovibrio spp. Thus, the results indicate potential for combining fermentation and anaerobic respiration for bioenergy production from photosynthetic biomass.     

分子生物学方法及其在海洋微生物生态中的应用

微生物在生态系统中起着独一无二的生态作用.微生物生态学的发展和工农业、环境保护及社会科学有着紧密的联系.海洋作为地球上最大的生境,孕育着大量的生物资源,是研究微生物生态的主要来源.综述微生物生态研究相关的分子生物学方法及海洋微生物生态的应用进展.     

关于微生物燃料电池底物的研究进展

近年来,微生物燃料电池已引起了广泛关注,它将低能量废水和木质纤维素生物质等有机废物转化为电能。在将来,微生物电能将成为一种重要的生物能源,因为微生物燃料电池提供了一种复合有机物和可再生生物能源中提取电能的可行性。人们研究了许多物质,以考察其是否能作为微生物电能转化的底物。这些物质包括人工的和天然废物,以及木质纤维素生物质。尽管现在微生物燃料电池提供的电流和功率较低,但是随着技术的发展和对微生物燃料电池系统的深入了解,微生物燃料电池转化的电流和电力将极大增加,从而向世人提供了一种可以将纤维素生物质和废水直接转化为有用能源的有效方法。本文介绍了迄今为止在微生物燃料电池中用到的各种反应底物,并对它们的应用效率和存在的不足进行了分析。     

Microbial Mannanases: An Overview of Production and Applications

ABSTRACT

Microbial mannanases have become biotechnologically important since they target the hydrolysis of complex polysaccharides of plant tissues into simple molecules like manno-oligosaccharides and mannoses. The role of mannanases in the paper and pulp industry is well established and recently they have found application in the food and feed technology, coffee extraction, oil drilling and detergent industry. Mannanses are enzymes produced mainly from microorganisms but mannanases produced from plants and animals have also been reported. Bacterial mannanases are mostly extracellular and can act in a wide range of pH and temperature, though acidic and neutral mannanases are more common. This review will focus on complex mannan structure and the microbial enzyme complex involved in its complete breakdown, mannanase sources, production conditions and their applications in the commercial sector. The reference to plant and animal mannanases has been made to complete the overview. However, the major emphasis of the review is on the microbial mannanases.     

Production of Microbial Cells from Hydrocarbons

Hydrocarbon-assimilating yeasts and bacteria were isolated from soil and sewage. The optimal conditions of cell yield from liquid paraffine by a Torulopsis yeast and a Pseudomonas strain were studied. A Torulopsis yeast gave, in optimal condition, 70 percent cell yield on a weight conversion basis from light oil fraction. In a strain of Pseudomonas the additions of amino acids, Fe^{+ +}, Mg^{+ +} and Ca^{+ +} ions were effective for cell production. This strain showed, in optimal condition, 80 percent cell yield (wt%) from kerosene.     

Generation of Electricity and Analysis of Microbial Communities in Wheat Straw Biomass-Powered Microbial Fuel Cells

Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity-producing microbial communities developed in two-chamber microbial fuel cells (MFCs) were investigated. The power density reached 123 mW/m² with an initial hydrolysate concentration of 1,000 mg chemical oxygen demand (COD)/liter, while coulombic efficiencies ranged from 37.1 to 15.5%, corresponding to the initial hydrolysate concentrations of 250 to 2,000 mg COD/liter. The suspended bacteria found were different from the bacteria immobilized in the biofilm, and they played different roles in electricity generation from the hydrolysate. The bacteria in the biofilm were consortia with sequences similar to those of Bacteroidetes (40% of sequences), Alphaproteobacteria (20%), Bacillus (20%), Deltaproteobacteria (10%), and Gammaproteobacteria (10%), while the suspended consortia were predominately Bacillus (22.2%). The results of this study can contribute to improving understanding of and optimizing electricity generation in microbial fuel cells.Wheat straw is one of the most abundant renewable resources. According to the Food and Agriculture Organization of the United Nations, approximately 1.9 × 10⁹ tons of wheat straw annually are produced worldwide, accompanied by 6.2 × 10⁸ tons of wheat production. Wheat straw is composed of 35 to 45% cellulose and 20 to 30% hemicelluloses with a relatively low lignin content (<20%) (42). The hemicellulose fraction of the straw is easily hydrolyzed to its constituent sugars by a hydrothermal treatment process, forming a carbohydrate-enriched liquid hydrolysate (46). Chemical and biological approaches to sustainable energy production from the liquefied hydrolysates to energy carriers, such as methane, ethanol, and H₂, have been developed. However, many of these approaches encounter technical and economical hurdles (10, 12, 15, 16). An alternative strategy is direct conversion of wheat straw biomass to electrical energy in microbial fuel cells (MFCs).MFCs are bioelectrochemical reactors in which microorganisms mediate the direct conversion of chemical energy stored in organic matter or bulk biomass into electrical energy (12, 15, 16, 40). Various substrates, such as simple carbohydrates, low-molecular-weight organic acids, starch, amino acids, chitin, cellulose, domestic wastewater, food-processing wastewater, recycled paper wastewater, and marine sediment organic matter, have been successfully utilized for power generation in MFCs (16-18, 27, 30, 33). To understand the microbial constraints on various fuel-powered MFCs, microbial communities have been characterized by several groups. Microbial communities from various systems are very different and often diverse, ranging from well-known metal- and anode-reducing bacteria to unknown exoelectrogens (1, 20, 21). It has been found that parameters such as the substrates used as fuels and the inocula used for starting up the MFCs can influence the anode bacterial communities in an MFC, which subsequently influence the efficiency of the MFCs (3, 14, 22, 38, 44). Different pure substrates, such as acetate, glucose, and lactate, were used as fuel to compare the microbial communities that developed in the MFCs. Regardless of the different substrates, all anode communities contained sequences closely affiliated with Geobacter sulfurreducens (>99% similarity) and an uncultured bacterium clone belonging to the family Bacteroidaceae (99% similarity). Firmicutes were only found in glucose-fed MFCs (20). Microbial-community analyses of MFCs powered with complex substrates have also been performed by several researchers, and their results were very diverse. The microbial community in starch wastewater-powered MFC was dominated by unidentified bacteria (35.9%), followed by Betaproteobacteria (25.0%), Alphaproteobacteria (20.1%), and the Cytophaga/Flexibacter/Bacteroides group (19.0%) (21). The anode-attached consortia in a cellulose-powered MFC were related to Clostridium spp., while Comamonas spp. were abundant in the suspended consortia (13). Although many studies have reported the microbial compositions of MFCs, it is still unclear which microbial communities develop as a function of the external parameters.Wheat straw biomass constitutes a large source for bioenergy production and shows promising prospects for electricity generation in MFCs. Therefore, wheat straw biomass was used to study the microbial communities that develop during the operation of an MFC in order to better understand the microbial electrochemical roles and potentially improve MFC performance.The objectives of this study were to (i) test wheat straw hydrolysate as a potential fuel in an MFC for electricity generation and (ii) study the microbial composition and evolution of electricity-producing communities in a two-chamber MFC system. Phylogenetic-diversity analysis of the enriched consortia was conducted to verify the presence of hydrolytic and respiratory anaerobes that could couple hydrolysate oxidation with proton reduction in the anode chamber. This is the first report of exploiting microbial communities for direct conversion of wheat straw hydrolysate to electrical energy in an MFC.     

Preparation of Encapsulated Microbial Cells for Environmental Applications

An improved method for the encapsulation of bacteria into microspheres of alginate, agarose, or polyurethane is described. Cell suspensions were passed through a low-pressure nozzle into an aqueous phase where matrix polymerization or gelation yielded beads 2 to 50 μm in diameter. Trials with a chlorophenol-degrading Flavobacterium species showed that cells entrapped by these procedures were as catabolically active as free cells. These types of beads should have numerous applications in the fields of environmental science and engineering.     

Digestion of Algal Biomass for Electricity Generation in Microbial Fuel Cells

We developed a semi-automated genome analysis system called GAMBLER in order to support the current whole-genome sequencing project focusing on alkaliphilic Bacillus halodurans C-125. GAMBLER was designed to reduce the human intervention required and to reduce the complications in annotating thousands of ORFs in the microbial genome. GAMBLER automates three major routines: analyzing assembly results provided by genome assembler software, assigning ORFs, and homology searching. GAMBLER is equipped with an interface for convenience of annotation. All processes and options are manipulatable through a WWW browser that enables scientists to share their genome analysis results without choosing computer platforms.     

微生物几丁质酶研究进展及应用*

几丁质由N-乙酰-D-氨基葡萄糖聚合而成,是自然界中仅次于纤维素的第二大类聚合物。微生物几丁质酶来源丰富,是生物降解或利用几丁质的主要媒介。野生型菌株几丁质酶产量低、活性弱,故近年来有关几丁质酶的研究侧重于对其产量及催化活性的提升等方面。此外,几丁质酶具有水解病原真菌细胞壁、破坏害虫体壁、生产N-乙酰氨基葡萄糖寡聚体或单体的应用价值,在医药、农业、食品加工等领域表现出巨大的市场潜力。综述微生物几丁质酶的来源、分类及工程改造,为后续几丁质酶的研究及开发利用提供参考。     

Phylogenetic and Metagenomic Analyses of Substrate-Dependent Bacterial Temporal Dynamics in Microbial Fuel Cells

Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m² to 140±11 mW/m², accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.     

微生物燃料电池中产电微生物的研究进展

产电微生物是微生物燃料电池系统的核心组成, 本文从生物学角度介绍了几种产电微生物的分类学地位、形态特征、生理生化特征及在微生物燃料电池中的产电机理和产电能力, 分析了利用产电微生物进行废水处理同时生物发电的应用前景, 提出产电微生物在MFC系统中的进一步研究方向为微生物的富集、驯化、改造和多种菌种优化组合等。     

Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells

In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.     

Electricity Generation in Microbial Fuel Cells Using Neutral Red as an Electronophore

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. In microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator (3.5 mA) was 10-fold more than the amount produced when thionin was the electron mediator (0.4 mA). The amount of electrical energy generated (expressed in joules per mole of substrate) and the amount of current produced from glucose (expressed in milliamperes) in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge (i.e., a mixed culture of anaerobic bacteria) was used in the fuel cell, stable (for 120 h) and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Our results are discussed in relation to factors that may improve the relatively low electrical efficiencies (1.2 kJ/mol) obtained with microbial fuel cells.     

沉积型海底微生物燃料电池构建及其影响因素研究

海底微生物燃料电池具有底物丰富、可长期运行、维护成本低和环境友好等特点,具有很好的研究价值和广阔的发展前景。但由于其低的功率密度输出和长期运行的不稳定性,使海底微生物燃料电池尚未得到广泛地实际应用。选取海底沉积泥用于实验室构建的海底微生物燃料电池装置中,比较了在不同阳极材料、阴阳极面积比、阳极修饰、阳极泥下深度条件下海底微生物燃料电池的功率密度输出及其电化学性能,得出最佳的海底微生物燃料电池阳极材料为碳毡;阴极及电极最佳面积比为1∶1;最佳阳极修饰为氨水浸渍;最佳阳极泥下深度为2 cm。