Microbiological degradation of pesticides in yard waste composting.

Changes in public opinion and legislation have led to the general recognition that solid waste treatment practices must be changed. Solid-waste disposal by landfill is becoming increasingly expensive and regulated and no longer represents a long-term option in view of limited land space and environmental problems. Yard waste, a significant component of municipal solid waste, has previously not been separated from the municipal solid-waste stream. The treatment of municipal solid waste including yard waste must urgently be addressed because disposal via landfill will be prohibited by legislation. Separation of yard waste from municipal solid waste will be mandated in many localities, thus stressing the importance of scrutinizing current composting practices in treating grass clippings, leaves, and other yard residues. Yard waste poses a potential environmental health problem as a result of the widespread use of pesticides in lawn and tree care and the persistence of the residues of these chemicals in plant tissue. Yard waste containing pesticides may present a problem due to the recalcitrant and toxic nature of the pesticide molecules. Current composting processes are based on various modifications of either window systems or in-vessel systems. Both types of processes are ultimately dependent on microbial bioconversions of organic material to innocuous end products. The critical stage of the composting process is the thermophilic phase. The fate and mechanism of removal of pesticides in composting processes is largely unknown and in need of comprehensive analysis.     

Fermentation of glycerol and production of valuable chemical and biofuel molecules

Glycerol has attracted the attention of scientific and industrial communities due to its generation in bulk quantities as a byproduct of biofuel industries. With the rapid growth of these industries in recent years, glycerol is frequently treated as a very low-value byproduct or even a waste product with a disposal cost associated to it. Glycerol is not only abundant and inexpensive but also can generate more reducing equivalents than glucose or xylose. This unique characteristic of glycerol offers a tremendous opportunity for its biological conversion to valuable products at higher yield. This review focuses on research efforts to utilize glycerol as a carbon source for the production of a variety of fuels and chemicals by both native and metabolically engineered microorganisms.     

国外环境生物技术的发展和展望

环境生物技术在社会的发展中起着越来越重要的积极作用,相关产业也随之迅速发展起来,环境治理要依赖对生物,尤其是微生物及其生理,生化特性的了解和认识,从而可以对其生理,生化和遗传方面的性能加以利用。在这方面,分离解毒微生物及阐明毒物降解过程和机理仍是现在研究的焦点,与此同时,对遗传基因方面的研究和利用还有许多研究工作待进行,监测和跟踪微生物已进入到了分子水平,而传感监测方面已有一些可喜的成果正在向生产转化,生物修复作为消除污染的手段正治理中发挥巨大的作用,但环境保护的根本应是在于进行无污染产生的生产,也称之为绿色生产,未来的社会中,环境生物技术仍对将社会产生巨大的影响,对环境保护起到重要的作用,特别是在新型生物能源的开发和探索方面,本文同时也对世界不同地区在环境生物技术的发展及其特点进行了综述。     

Industrial bioconversion of renewable resources as an alternative to conventional chemistry

There are numerous possibilities for replacing chemical techniques with biotechnological methods based on renewable resources. The potential of biotechnology (products, technologies, metabolic pathways) is for the most part well known. Often the costs are still the problem. Biotechnological advances have the best chances for replacing some fine chemicals. While the raw material costs are less of a consideration here, the environmental benefit is huge, as chemical-technical processes often produce a wide range of undesirable/harmful by-products or waste. In the case of bulk chemicals (<US $1/kg) the product price is affected mainly by raw material costs. As long as fossil raw materials are still relatively inexpensive, alternatives based on renewable resources cannot establish themselves. Residues and waste, which are available even at no cost in some cases, are an exception. The introduction of new technologies for the efficient use of such raw materials is currently being promoted. The utilisation of residual wood, plant parts, waste fat, and crude glycerol, for example, provides great potential. For industrial chemicals (US $2–4/kg), process and recovery costs play a greater role. Here, innovative production technologies and product recovery techniques (e.g. on-line product separation) can increase competitiveness.     

On the use of oxygenic photosynthesis for the sustainable production of commodity chemicals

A sustainable society will have to largely refrain from the use of fossil carbon deposits. In such a regime, renewable electricity can be harvested as a primary source of energy. However, as for the synthesis of carbon‐based materials from bulk chemicals, an alternative is required. A sustainable approach towards this is the synthesis of commodity chemicals from CO₂, water and sunlight. Multiple paths to achieve this have been designed and tested in the domains of chemistry and biology. In the latter, the use of both chemotrophic and phototrophic organisms has been advocated. ‘Direct conversion’ of CO₂ and H₂O, catalyzed by an oxyphototroph, has excellent prospects to become the most economically competitive of these transformations, because of the relative ease of scale‐up of this process. Significantly, for a wide range of energy and commodity products, a proof of principle via engineering of the corresponding production organism has been provided. In the optimization of a cyanobacterial production organism, a wide range of aspects has to be addressed. Of these, here we will put our focus on: (1) optimizing the (carbon) flux to the desired product; (2) increasing the genetic stability of the producing organism and (3) maximizing its energy conversion efficiency. Significant advances have been made on all these three aspects during the past 2 years and these will be discussed: (1) increasing the carbon partitioning to >50%; (2) aligning product formation with the growth of the cells and (3) expanding the photosynthetically active radiation region for oxygenic photosynthesis.     

Saccharomyces cerevisiae: a potential host for carboxylic acid production from lignocellulosic feedstock?

Carboxylic acids are important bulk chemicals that can be used as building blocks for the production of polymers, as acidulants, preservatives and flavour compound or as precursors for the synthesis of pharmaceuticals. Today, their production mainly takes place through catalytic processing of petroleum-based precursors. An appealing alternative would be to produce these compounds from renewable resources, using tailor-made microorganisms. Saccharomyces cerevisiae has already demonstrated its value for bioethanol production from renewable resources. In this review, we discuss Saccharomyces cerevisiae engineering potential, current strategies for carboxylic acid production as well as the specific challenges linked to the use of lignocellulosic biomass as carbon source.     

Improving the ‘tool box’ for robust industrial enzymes

The speed of sequencing of microbial genomes and metagenomes is providing an ever increasing resource for the identification of new robust biocatalysts with industrial applications for many different aspects of industrial biotechnology. Using ‘natures catalysts’ provides a sustainable approach to chemical synthesis of fine chemicals, general chemicals such as surfactants and new consumer-based materials such as biodegradable plastics. This provides a sustainable and ‘green chemistry’ route to chemical synthesis which generates no toxic waste and is environmentally friendly. In addition, enzymes can play important roles in other applications such as carbon dioxide capture, breakdown of food and other waste streams to provide a route to the concept of a ‘circular economy’ where nothing is wasted. The use of improved bioinformatic approaches and the development of new rapid enzyme activity screening methodology can provide an endless resource for new robust industrial biocatalysts.This mini-review will discuss several recent case studies where industrial enzymes of ‘high priority’ have been identified and characterised. It will highlight specific hydrolase enzymes and recent case studies which have been carried out within our group in Exeter.

     

Metabolomics-assisted synthetic biology

As the world progresses from a fossil-fuel based economy to a more sustainable one, synthetic biology will become increasingly important for the production of high-value fine chemicals as well as low-value commodities in bulk. The integration of metabolomics and fluxomics within synthetic biology projects will be vital at all levels, including the initial design of the pathways to be generated, through to the optimisation of those pathways so that more efficient conversion of low-cost starting materials into highly desirable products can be achieved. This review highlights these areas and details the most important and exciting advances being made in this area.     

酿酒酵母细胞器区室化合成化学品的研究进展

公认食品安全的酿酒酵母(Saccharomyces cerevisiae)是合成生物学中被广泛研究的底盘细胞,常作为生产高值或大宗化学品的微生物细胞工厂。近年来,通过各种代谢工程改造策略,已有大量化学品的合成途径在酿酒酵母中建立并优化,且部分化学品具备了产业化价值。作为真核生物,酿酒酵母具有完整的细胞内膜系统及其组成的复杂细胞器区室,而这些细胞器区室往往含有某些化学品合成所必需的较高浓度前体底物(如线粒体中的乙酰辅酶A),或更加充足的酶、辅因子、能量等,可为目标产物的生物合成提供更适宜的物理、化学环境,但同时不同细胞器的结构特点有时也成为特定化合物合成的障碍。为此,研究人员在深入分析不同细胞器自身特点的基础上,结合目标化学品合成途径与细胞器之间的适配度,对细胞器开展了大量针对性改造工作以提高产物合成效率。本文详细综述了酿酒酵母中线粒体、过氧化物酶体、高尔基体、内质网、脂滴和液泡等细胞器的途径改造及优化策略,以及利用细胞器区室化合成化学品的研究进展,并对目前存在的困难和挑战以及未来研究方向进行了总结与展望。     

Production of fuels and chemicals from renewable resources using engineered Escherichia coli

Biotechnological production of fuels and chemicals from renewable resources is an appealing way to move from the current petroleum-based economy to a biomass-based green economy. Recently, the feedstocks that can be used for bioconversion or fermentation have been expanded to plant biomass, microbial biomass, and industrial waste. Several microbes have been engineered to produce chemicals from renewable resources, among which Escherichia coli is one of the best studied. Much effort has been made to engineer E. coli to produce fuels and chemicals from different renewable resources. In this paper, we focused on E. coli and systematically reviewed a range of fuels and chemicals that can be produced from renewable resources by engineered E. coli. Moreover, we proposed how can we further improve the efficiency for utilizing renewable resources by engineered E. coli, and how can we engineer E. coli for utilizing alternative renewable feedstocks. e.g. C1 gases and methanol. This review will help the readers better understand the current progress in this field and provide insights for further metabolic engineering efforts in E. coli.     

Microbial CO Conversions with Applications in Synthesis Gas Purification and Bio-Desulfurization

ABSTRACT

Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO₂-neutral) biomass. The conversion of CO with H₂O to CO₂ and H₂ is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization of wastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.     

Microbiological aspects of the removal of chlorinated hydrocarbons from air

Chlorinated hydrocarbons are widely used synthetic chemicals that are frequently present in industrial emissions. Bacterial degradation has been demonstrated for several components of this class of compounds. Structural features that affect the degradability include the number of chlorine atoms and the presence of oxygen substituents. Biological removal from waste streams of compounds that serve as a growth substrate can relatively easily be achieved. Substrates with more chlorine substituents can be converted cometabolically by oxidative routes. The microbiological principles that influence the biodegradability of chlorinated hydrocarbons are described. A number of factors that will determine the performance of microorganisms in systems for waste gas treatment is discussed. Pilot plant evaluations, including economics, of a biological trickling filter for the treatment of dichloromethane containing waste gas indicate that at least for this compound biological treatment is cost effective.     

A continuous biological process to decolorize bleach plant effluents

Although almost every U.S. pulp mill has a biological wastewater treatment system, these systems based on bacteria, are largely ineffective in the removal of color. For this reason, we have attempted to utilize Phanerochaete chrysosporium, a fungus known to degrade lignin, as the primary organism in a novel waste treatment scheme named the MyCoR Process. Color from bleached Kraft mills originates principally from the first extraction stage of the bleach plant. It is this waste stream which is sent to the MyCoR Process reactor, a rotating biological contactor, for decolorization. We have found that under optimal conditions up to 2,000 color units/L/day can be removed from the waste stream. There is also a concomitant removal of COD and BOD. In addition, chlorolignins originating from the bleaching process were found to be dechlorinated; this is of interest to those concerned with the impact of bleach plant effluents on the environment. The process uses conventional wastewater treatment equipment. However, the use of a pure culture of fungus in a secondary metabolic state has not been attempted previously in a waste treatment scheme. Minor equipment modification and close operator attention may therefore be required. A preliminary economic analysis shows that the MyCoR Process, in its present state, would cost about US$30/metric ton of bleached Kraft pulp produced. This cost will decrease as improved or new strains of fungi are developed for the process.     

Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization

Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO2-neutral) biomass. The conversion of CO with H2O to CO2 and H2 is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization ofwastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.     

Production of ethanol,organic acids and hydrogen: an opportunity for mixed culture biotechnology?

Anaerobic fermentation of biodegradable organic materials is usually carried out to obtain the final product, methane, a valuable energy source. However, it is also well known that various intermediates are produced in this process, e.g. ethanol, volatile organic acids and hydrogen. All these species have applications and value as fuels or chemicals. This paper shows a critical analysis of the potential of using anaerobic fermentation by mixed cultures to produce intermediates, e.g. ethanol, acetic, lactic and butyric acid and hydrogen, rather than methane. This paper discusses the current processes to produce these chemicals and compares them with the alternative approach of using open mixed cultures to produce them simultaneously via fermentation from renewable resources. None of these chemicals is currently produced via mixed culture fermentation: ethanol and lactic acid are usually produced in pure culture fermentation using food crops, e.g. corn or sugar cane, as starting materials; hydrogen, acetic and butyric acids are mainly produced via chemical synthesis from fossil fuel derived starting materials. A possible flow-sheet for the production of these chemicals from organic waste using mixed culture fermentation is proposed and the advantages and disadvantages of this process compared to current processes are critically discussed. The paper also discusses the research challenges which need to be addressed to make this process feasible.     

Practical application of synthetic biology principles

Synthetic biology can be defined as the “repurposing and redesign of biological systems for novel purposes or applications, ” and the field lies at the interface of several biological research areas. This broad definition can be taken to include a variety of investigative endeavors, and successful design of new biological paradigms requires integration of many scientific disciplines including (but not limited to) protein engineering, metabolic engineering, genomics, structural biology, chemical biology, systems biology, and bioinformatics. This review focuses on recent applications of synthetic biology principles in three areas: (i) the construction of artificial biomolecules and biomaterials; (ii) the synthesis of both fine and bulk chemicals (including biofuels); and (iii) the construction of “smart” biological systems that respond to the surrounding environment.     

Production and applications of carbohydrate-derived sugar acids as generic biobased chemicals

This review considers the chemical and biotechnological synthesis of acids that are obtained by direct oxidation of mono- or oligosaccharide, referred to as sugar acids. It focuses on sugar acids which can be readily derived from plant biomass sources and their current and future applications. The three main classes of sugar acids are aldonic, aldaric and uronic acids. Interest in organic acids derived from sugars has recently increased, as part of the interest to develop biorefineries which produce not only biofuels, but also chemicals to replace those currently derived from petroleum. More than half of the most desirable biologically produced platform chemicals are organic acids. Currently, the only sugar acid with high commercial production is d-gluconic acid. However, other sugar acids such as d-glucaric and meso-galactaric acids are being produced at a lower scale. The sugar acids have application as sequestering agents and binders, corrosion inhibitors, biodegradable chelators for pharmaceuticals and pH regulators. There is also considerable interest in the use of these molecules in the production of synthetic polymers, including polyamides, polyesters and hydrogels. Further development of these sugar acids will lead to higher volume production of the appropriate sugar acids and will help support the next generation of biorefineries.     

Short-term effects of aerially-applied fire-suppressant foams on water chemistry and macroinvertebrates in streams after natural wild-fire on Kangaroo Island, South Australia

In remote areas, wild-fires often must be controlled by applying fire-retardants and suppressants dropped from small aircraft. However, impacts of these chemicals on natural stream ecosystems are poorly known. Unintentional aerial application of fire-fighting chemicals (Phos-Chek WD-881 and ForExspan S) onto two small streams during a natural wildfire on Kangaroo Island, South Australia, provided an opportunity to study the short-term effects on water chemistry and aquatic invertebrates. Within 2 weeks of application, samples of water and macroinvertebrates were collected from sites upstream of the application point, within the zone of application, and downstream where burning had been controlled on two streams. Three sites on a reference stream in the same sub-catchment that had been burned by the same fire but without application of fire-suppressants were also sampled. All sites were resampled three months later (within two weeks of the first flushing rains). There were no marked differences in water quality among the sites on the reference stream but in one of the impacted streams where flow had ceased before the fire, dissolved and total phosphorus concentrations were elevated at the site where the fire-suppressants were applied. Phosphorus concentrations were reduced 2–3-fold at this site after brief flushing by rain. Conversely, dissolved and total N and P concentrations at the other impacted stream that flowed permanently did not differ among the sites and there was no evidence for persistent changes to water quality from the applied fire-suppressant foams. Taxon richness was higher at the application and downstream sites than at upstream sites in the two impacted streams. There were also no discernible effects of the fire-suppressants on macroinvertebrate assemblage composition or taxon richness within the two streams two weeks after the chemical application or soon after flushing rains. Assemblage composition in the temporary stream was significantly different from that in the reference and the other impacted stream but also appeared unaffected by the fire-suppressants. The lack of impact on resident stream macroinvertebrates may result partly from their inherent high tolerance to the harsh physical and chemical conditions of these streams, many of which typically cease flow in summer.     

Chemical-based fecal source tracking methods: current status and guidelines for evaluation

Fecal source tracking is a rapidly evolving field for which there have been a number of method evaluation studies, workshops, review articles and a book that synthesize information about method efficacy. Chemicals that are specific to human wastewater offer several potential advantages over biologically based methods, but have received less scrutiny. More than 35 chemical analytes have been found to consistently occur in human waste streams and here we review these potential human-origin indicators in context of seven evaluation criteria. Some chemical methods offer advantages over microbial methods: they are generally faster to prepare and analyze, more source-specific because they are not confounded by regrowth in the environment, and some may be more geographically and temporally stable. However, they often require specialized equipment and are usually more expensive regarding sample preparation and analysis. Additionally, most chemicals that are specific to human waste-streams occur at concentrations low enough to be diluted below detection limits once the waste-stream enters the ambient environment. These two factors will likely result in chemical measures being used more often as cross-validation supplements or initial screening approaches, rather than replacements for microbial measures. Cross-validation supplements include several chemicals that are highly specific to human sources and can be important contributors when certainties about human sources are critical, such as in drinking water applications. At least one set of chemicals, fecal sterols and stanols, may have potential for identification of other sources in addition to humans. Of all the chemicals examined to date, optical brighteners (OBs) in detergents have shown considerable promise, especially for screening purposes. Optical brighteners are not as sensitive as most microbial assessments, but can be measured with a hand-held fluorometer, providing near real-time and relatively inexpensive tracking of signals in the field, if the human fecal source contains an OB concentration large enough to produce a measurable signal.