Microbial production of amino acids and derived chemicals: Synthetic biology approaches to strain development

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Microbial production of diols as platform chemicals: recent progresses

Diols are chemicals with two hydroxyl groups which have a wide range of appealing applications as chemicals and fuels. In particular, four diol compounds, namely 1,3-propanediol (1,3-PDO), 1,2-propanediol (1,2-PDO), 2,3-butanediol (2,3-BDO) and 1,4-butanediol (1,4-BDO) can be biotechnologically produced by direct microbial bioconversion of renewable materials. These diols are considered as platform green chemicals. We review and discuss here the recent development in the microbial production of these diols, especially regarding the engineering of production strains and optimization of the fermentation processes.     

Microbial production of chemicals driven by CRISPR-Cas systems

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Microbial production of fatty acid-derived fuels and chemicals

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Microbial production of fatty acids and derivative chemicals

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Microbial production of building block chemicals and polymers

Owing to our increasing concerns on the environment, climate change, and limited natural resources, there has recently been considerable effort exerted to produce chemicals and materials from renewable biomass. Polymers we use everyday can also be produced either by direct fermentation or by polymerization of monomers that are produced by fermentation. Recent advances in metabolic engineering combined with systems biology and synthetic biology are allowing us to more systematically develop superior strains and bioprocesses for the efficient production of polymers and monomers. Here, we review recent trends in microbial production of building block chemicals that can be subsequently used for the synthesis of polymers. Also, recent successful cases of direct one-step production of polymers are reviewed. General strategies for the production of natural and unnatural platform chemicals are described together with representative examples.     

Microbial production of lactic acid: the latest development

Lactic acid is an important platform chemical for producing polylactic acid (PLA) and other value-added products. It is naturally produced by a wide spectrum of microbes including bacteria, yeast and filamentous fungi. In general, bacteria ferment C5 and C6 sugars to lactic acid by either homo- or hetero-fermentative mode. Xylose isomerase, phosphoketolase, transaldolase, l- and d-lactate dehydrogenases are the key enzymes that affect the ways of lactic acid production. Metabolic engineering of microbial strains are usually needed to produce lactic acid from unconventional carbon sources. Production of d-LA has attracted much attention due to the demand for producing thermostable PLA, but large scale production of d-LA has not yet been commercialized. Thermophilic Bacillus coagulans strains are able to produce l-lactic acid from lignocellulose sugars homo-fermentatively under non-sterilized conditions, but the lack of genetic tools for metabolically engineering them severely affects their development for industrial applications. Pre-treatment of agriculture biomass to obtain fermentable sugars is a pre-requisite for utilization of the huge amounts of agricultural biomass to produce lactic acid. The major challenge is to obtain quality sugars of high concentrations in a cost effective-way. To avoid or minimize the use of neutralizing agents during fermentation, genetically engineering the strains to make them resist acidic environment and produce lactic acid at low pH would be very helpful for reducing the production cost of lactic acid.     

Microbial processes and bacterial populations associated to anaerobic treatment of sulfate-rich wastewater

A pilot-scale (1.2 m³) anaerobic sequencing batch biofilm reactor (ASBBR) containing mineral coal for biomass attachment was fed with sulfate-rich wastewater at increasing sulfate concentrations. Ethanol was used as the main organic source. Tested COD/sulfate ratios were of 1.8 and 1.5 for sulfate loading rates of 0.65–1.90 kgSO₄²⁻/cycle (48 h-cycle) or of 1.0 in the trial with 3.0 gSO₄²⁻ l⁻¹. Sulfate removal efficiencies observed in all trials were as high as 99%. Molecular inventories indicated a shift on the microbial composition and a decrease on species diversity with the increase of sulfate concentration. Beta-proteobacteria species affiliated with Aminomonas spp. and Thermanaerovibrio spp. predominated at 1.0 gSO₄²⁻ l⁻¹. At higher sulfate concentrations the predominant bacterial group was Delta-proteobacteria mainly Desulfovibrio spp. and Desulfomicrobium spp. at 2.0 gSO₄²⁻ l⁻¹, whereas Desulfurella spp. and Coprothermobacter spp. predominated at 3.0 gSO₄²⁻ l⁻¹. These organisms have been commonly associated with sulfate reduction producing acetate, sulfide and sulfur. Methanogenic archaea (Methanosaeta spp.) was found at 1.0 and 2.0 gSO₄²⁻ l⁻¹. Additionally, a simplified mathematical model was used to infer on metabolic pathways of the biomass involved in sulfate reduction.     

Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update

Anaerobic digestion technology is the biological treatment of organic waste and wastewater without input of external electron acceptors (oxygen), offering the potential to reduce treatment cost and to produce energy as 'biogas' (methane) from organic waste. The technology has become enormously popular in the past two decades, and knowledge of microbiological aspects of the technology has also accumulated significantly. Major advances have been made in elucidating the diversity of yet-to-be cultured microbes in anaerobic digestion processes, and the cultivation of uncultured organisms is of great interest with regard to gaining insights into the function of these organisms. In addition, recent advances have been made in the development of microbial fuel cells as an alternative, direct energy-yielding treatment system.     

Biocatalytic and fermentative production of useful chemicals by processes using methylotrophs

Abstract Processes for production of glycerol, aldehydes and polyols by using the methylotrophic function of yeasts were developed. The unique metabolism of glycerol involving a new enzyme, dihydroxyacetone reductase, was applied to the glycerol production employing a glycerol-negative mutant. Alcohol oxidase activity was improved and used for production of aldehydes from corresponding alcohols. NADH generation during methanol oxidation was coupled with hydrogenation of sugars to produce sorbitol, iditol and xylitol.     

Microbial production of bacteriocins: Latest research development and applications

Bacteriocins are low molecular weight peptides secreted by the predator bacterial cells to kill sensitive cells present in the same ecosystem competing for food and other nutrients. Exceptionally few bacteriocins along with their native antibacterial property also exhibit additional anti-viral and anti-fungal properties. Bacteriocins are generally produced by Gm+, Gm– and archaea bacteria. Bacteriocins from Gm?+?bacteria especially from lactic acid bacteria (LAB) have been thoroughly investigated considering their great biosafety and broad industrial applications. LAB expressing bacteriocins were isolated from fermented milk and milk products, rumen of animals and soil using deferred antagonism assay. Nisin is the only bacteriocin that has got FDA approval for application as a food preservative, which is produced by Lactococcus lactis subsp. Lactis. Its crystal structure explains that its antimicrobial properties are due to the binding of NH₂ terminal to lipid II molecule inhibiting the peptidoglycan synthesis and carboxy terminal forming pores in bacterial cell membrane leading to cell lysis. The hinge region connecting NH₂ and carboxy terminus has been mutated to generate mutant variants with higher antimicrobial activity. In a 50 ton fermentation of the mutant strain 3807 derived from L. lactis subsp. lactis ATCC 11454, 9,960?IU/mL of nisin was produced. Currently, high purity of nisin (>99%) is very expensive and hardly commercially available. Development of more advanced tools for cost-effective separation and purification of nisin would be commercially attractive. Chemical synthesis and heterologous expression of bacteriocins ended in low yields of pure proteins. At present, bacteriocins are almost solely applied in food industries, but they have a great potential to be used in other fields such as feeds, organic fertilizers, environmental protection and personal care products. The future of bacteriocins is largely dependent on getting FDA approval for use of other bacteriocins in addition to nisin to promote the research and applications.     

餐厨垃圾厌氧消化处理主要过程的微生物群落结构分析

【背景】厌氧消化是我国餐厨垃圾处理的主要方法,微生物在其处理过程中起到关键作用,但是目前对其不同工艺单元微生物群落结构的研究较少。【目的】通过分析各工艺单元的微生物多样性与群落结构,为改进餐厨垃圾资源化处理技术、提高资源利用效率提供科学依据。【方法】采集某餐厨垃圾处理厂油水分离、厌氧发酵、沼渣脱水等3个工艺单元产生的废液样品,采用16S rRNA基因高通量测序技术,研究其菌群组成、丰度、优势菌群及其与环境因子的相关性。【结果】初始油水分离样品中的微生物群落种类相对较少,而经厌氧发酵和沼渣脱水处理后样品中的微生物群落种类较丰富。在门水平上,厚壁菌门(Firmicutes)在各单元样品中所占平均比例最高,为81.1%,其次为拟杆菌门(Bacteroidetes)和绿弯菌门(Chloroflexi),分别占15.81%和4.59%;在属水平上,相对丰度较高的菌属为乳酸菌属(Lactobacillus)、互营单胞菌属(Syntrophomonas)等。餐厨垃圾处理过程中的部分菌属可能具有资源-环境双重属性,例如在沼渣脱水单元相对丰度高达32.67%的假单胞菌属(Pseudomonas),该菌属中既存在少部分致病菌或条件致病菌,也具有生产聚羟基脂肪酸酯的功能菌。影响各组样品微生物群落组成结构最显著的因子是p H值,其次是总糖的含量。【结论】研究明确了典型餐厨垃圾厌氧消化处理工艺单元的微生物群落结构和多样性,并提出了优化处理工艺、强化资源利用效率的建议。     

Microbial and enzymatic processes for the production of pharmacologically important nucleosides

S-Adenosylmethionine, S-adenosylhomocysteine and related nucleosides have recently attracted great interest as key regulatory compounds in many biological transmethylation systems. Although these nucleosides in the pharmacological and chemotherapeutic fields have great potential, no process for their practical production has been developed yet. One of the problems is in the elucidation of the complex relationships between these nucleosides and the control mechanisms of biological transmethylations. This review shows, however, that some of these useful compounds can now be very easily produced by microbial or enzymatic processes.     

Potential errors in the quantitative evaluation of biogas production in anaerobic digestion processes

Errors that are commonly made in the quantification of biogas from anaerobic digestion experiments were investigated.For liquid displacement gasometers where a barrier solution separates the biogas and the atmosphere, inaccuracy due to gas diffusion was examined experimentally. Acidified saturated saline solution was the most suitable barrier solution, as biogas characteristics changed least with time. Using acidified or tap water caused considerable biogas losses and should therefore be avoided where biogas is stored before measurement.Errors associated with volume calculation from three common liquid displacement gasometer types were investigated theoretically. Corrections that must be made to obtain gas volumes at standard temperature and pressure when using this equipment are discussed. Regarding experimental errors, gasometer designs where displaced liquid is weighed to determine the volume are the most versatile since errors depend mainly upon balance sensitivity. Using liquid heights to calculate volume requires appropriate sizing of the gasometer relative to the volume of gas measured.The calibration of a low flow gas meter was investigated and an approximately linear variation with flow rate was found; hence in situ calibration is advised for this type of instrument. Correction for atmospheric conditions should be performed in real time to reduce errors.     

Microbial hydrogen production with Bacillus coagulans IIT-BT S1 isolated from anaerobic sewage sludge

Bacillus coagulans strain IIT-BT S1 isolated from anaerobically digested activated sewage sludge was investigated for its ability to produce H(2) from glucose-based medium under the influence of different environmental parameters. At mid-exponential phase of cell growth, H(2) production initiated and reached maximum production rate in the stationary phase. The maximal H(2) yield (2.28 mol H(2)/molglucose) was recorded at an initial glucose concentration of 2% (w/v), pH 6.5, temperature 37 degrees C, inoculum volume of 10% (v/v) and inoculum age of 14 h. Cell growth rate and rate of hydrogen production decreased when glucose concentration was elevated above 2% w/v, indicating substrate inhibition. The ability of the organism to utilize various carbon sources for H(2) fermentation was also determined.