微生物对低温极端环境适应性的研究进展

嗜冷微生物是地球寒冷环境中最主要的生物类群,并且是驱动全球生物地球化学循环的关键环节。嗜冷微生物在适应策略上显示出应对多种极端环境因素的巨大潜力,研究其适应和进化机制有助于更好地理解微生物与环境之间相互作用过程,并有效利用极端环境微生物资源。近年来,随着分子生物学和基因组学技术的高速发展,对微生物适应寒冷环境的机制及嗜冷微生物在指示气候变化和工农业应用方面均有一系列的突破。在此,本文将从基因组的GC含量、蛋白质稳定性、转录翻译调控、细胞膜流动性、渗透压调节、抗氧化损失和基因组适应性进化等方面总结当前在微生物适应低温环境机制上所取得的进展,并展望低温环境微生物在指示气候变化和工农业应用中的前景。     

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.     

工业微生物：创新与突破专刊序言(2021)

工业微生物及其产品广泛用于工业、农业、医药等诸多领域,相关产业在国民经济中具有举足轻重的地位。高效的菌株是提高生产效率的核心,而先进发酵技术和仪器平台对充分开发菌株代谢潜能也很重要。近年来,工业微生物领域的研究取得了快速进展,人工智能、高效基因组编辑技术和合成生物学技术逐渐广泛使用,相关产业应用也在不断扩展。为进一步促进工业微生物在生物制造等领域的应用,《生物工程学报》特组织出版专刊,从微生物菌株的多样性和生理代谢、菌株改造技术、发酵过程优化和放大,高通量微液滴培养装备开发以及工业微生物应用等方面,分别阐述目前的研究进展,并展望未来的发展趋势,为促进工业微生物及生物制造等产业的发展奠定基础。     

不同环境条件下土壤微生物对模拟大气氮沉降的响应

研究了林内及林缘两个生境中,在有苔藓覆盖和无苔藓覆盖条件下,人工加氮对土壤理化性质及土壤微生物群落的影响。结果显示加氮使土壤pH下降,有效态氮和有效态磷的含量上升,但不同生境及有无苔藓植物覆盖在一定程度上影响土壤理化性质及其对加氮的反应。苔藓植物覆盖可以缓解加氮引起的土壤酸化及有效氮含量上升压力,促进有效态磷含量上升。不同生境中,土壤微生物对氮沉降的响应亦不同。低氮使林缘生境土壤微生物的胁迫程度减小,中高氮使其胁迫程度上升,而任何加氮均增加林内生境中土壤微生物的胁迫程度。两个生境中,苔藓植物覆盖均可以缓解过量氮沉降对土壤微生物造成的压力,降低过量氮沉降对土壤微生物的伤害,提高土壤微生物的代谢活性。     

Molecular Adaptation Mechanisms Employed by Ethanologenic Bacteria in Response to Lignocellulose-derived Inhibitory Compounds

Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of ''intelligent'' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains.     

Biotechnological production of eicosapentaenoic acid: From a metabolic engineering point of view

Eicosapentaenoic acid (EPA) is an ω3 polyunsaturated fatty acid which has been demonstrated to play important roles in a number of aspects of human health. EPA is traditionally obtained from marine fish oils. However, the shrinking fish populations are making the sustainability of these sources questionable. Consequently, alternative sources of EPA are being sought, especially from marine microalgae, bacteria, and fungi. These microorganisms contain relatively large amounts of high-quality EPA and they are the primary producers of this important fatty acid. There are two distinct pathways for EPA de novo biosynthesis in microbial systems: the desaturation and elongation pathway and the polyketide pathway. Genes involved in the biosynthetic pathways have been identified from different microorganisms and characterized in depth. In addition, numerous strategies have been developed for commercial production of EPA by microbial fermentation, among which strain improvements by genetic engineering could provide high-yield producers of EPA. In this review, we summarize recent efforts and experiences devoted to metabolic engineering of various microorganisms that lead to efficient biocatalysts for the production of EPA, as well as the key limitations and challenges. The combination of traditional biochemistry and molecular biology with new systems biology and synthetic biology tools will provide a better view of EPA biosynthesis and a greater potential of microbial production. Continued advances in metabolic engineering will help to improve the final titer, productivity, and yield of EPA.     

环境微生物不依赖于培养的基因组学研究及应用

微生物在生物圈中分布广泛,并且在地球物质循环中占有重要地位,但是约99﹪的微生物目前还不能通过传统的培养方法得到纯培养物（即未培养微生物）,给这些未培养微生物的研究带来很大的困难。随着分子生物学的快速发展及其在微生物研究中的广泛运用,促进了以环境中未培养微生物为研究对象的新兴学科--环境基因组学的产生和发展。在不进行相关微生物培养分离的情况下,通过从环境样品中直接提取获得所有微小生物的全部遗传物质,并构建环境基因组文库;进一步利用功能基因组学研究策略,从文库中寻找编码产生新的有生物活性产物的基因;通过对系统发育相关锚定位点基因序列分析,从而确定特定生态环境体系中未培养微生物的种类结构组成及进化地位,并最终重建该体系中微生物群体的基本物质循环模式。此外,环境基因组学也可以在对未培养微生物生理生化特性深入了解的基础上,建立发展合适的培养体系,最终获得某些特定微生物的纯培养物。本文对环境基因组的构建及相关分析研究策略的进展进行了综述;同时介绍了其在微生物分类及生态学研究的应用。     

Influence of growth temperature on the production of antibody Fab fragments in different microbes: a host comparative analysis

Microorganisms encounter diverse stress conditions in their native habitats but also during fermentation processes, which have an impact on industrial process performance. These environmental stresses and the physiological reactions they trigger, including changes in the protein folding/secretion machinery, are highly interrelated. Thus, the investigation of environmental factors, which influence protein expression and secretion is still of great importance. Among all the possible stresses, temperature appears particularly important for bioreactor cultivation of recombinant hosts, as reductions of growth temperature have been reported to increase recombinant protein production in various host organisms. Therefore, the impact of temperature on the secretion of proteins with therapeutic interest, exemplified by a model antibody Fab fragment, was analyzed in five different microbial protein production hosts growing under steady-state conditions in carbon-limited chemostat cultivations. Secretory expression of the heterodimeric antibody Fab fragment was successful in all five microbial host systems, namely Saccharomyces cerevisiae, Pichia pastoris, Trichoderma reesei, Escherichia coli and Pseudoalteromonas haloplanktis. In this comparative analysis we show that a reduction of cultivation temperature during growth at constant growth rate had a positive effect on Fab 3H6 production in three of four analyzed microorganisms, indicating common physiological responses, which favor recombinant protein production in prokaryotic as well as eukaryotic microbes.     

Microbial responses to environmental arsenic

Microorganisms have evolved dynamic mechanisms for facing the toxicity of arsenic in the environment. In this sense, arsenic speciation and mobility is also affected by the microbial metabolism that participates in the biogeochemical cycle of the element. The ars operon constitutes the most ubiquitous and important scheme of arsenic tolerance in bacteria. This system mediates the extrusion of arsenite out of the cells. There are also other microbial activities that alter the chemical characteristics of arsenic: some strains are able to oxidize arsenite or reduce arsenate as part of their respiratory processes. These type of microorganisms require membrane associated proteins that transfer electrons from or to arsenic (AoxAB and ArrAB, respectively). Other enzymatic transformations, such as methylation-demethylation reactions, exchange inorganic arsenic into organic forms contributing to its complex environmental turnover. This short review highlights recent studies in ecology, biochemistry and molecular biology of these processes in bacteria, and also provides some examples of genetic engineering for enhanced arsenic accumulation based on phytochelatins or metallothionein-like proteins.     

Using the stress response to monitor process control: pathways to more effective bioremediation

Environmental contamination with a variety of pollutants has prompted the development of effective bioremediation strategies. But how can these processes be best monitored and controlled? One avenue under investigation is the development of stress response systems as tools for effective and general process control. Although the microbial stress response has been the subject of intensive laboratory investigation, the environmental reflection of the laboratory response to specific stresses has been little explored. However, it is only within an environmental context, in which microorganisms are constantly exposed to multiple changing environmental stresses, that there will be full understanding of microbial adaptive resiliency. Knowledge of the stress response in the environment will facilitate the control of bioremediation and other processes mediated by complex microbial communities.     

Metabolic engineering for the synthesis of polyesters: A 100-year journey from polyhydroxyalkanoates to non-natural microbial polyesters

As concerns increase regarding sustainable industries and environmental pollutions caused by the accumulation of non-degradable plastic wastes, bio-based polymers, particularly biodegradable plastics, have attracted considerable attention as potential candidates for solving these problems by substituting petroleum-based plastics. Among these candidates, polyhydroxyalkanoates (PHAs), natural polyesters that are synthesized and accumulated in a range of microorganisms, are considered as promising biopolymers since they have biocompatibility, biodegradability, and material properties similar to those of commodity plastics. Accordingly, substantial efforts have been made to gain a better understanding of mechanisms related to the biosynthesis and properties of PHAs and to develop natural and recombinant microorganisms that can efficiently produce PHAs comprising desired monomers with high titer and productivity for industrial applications.Recent advances in biotechnology, including those related to evolutionary engineering, synthetic biology, and systems biology, can provide efficient and effective tools and strategies that reduce time, labor, and costs to develop microbial platform strains that produce desired chemicals and materials. Adopting these technologies in a systematic manner has enabled microbial fermentative production of non-natural polyesters such as poly(lactate) [PLA], poly(lactate-co-glycolate) [PLGA], and even polyesters consisting of aromatic monomers from renewable biomass-derived carbohydrates, which can be widely used in current chemical industries.In this review, we present an overview of strain development for the production of various important natural PHAs, which will give the reader an insight into the recent advances and provide indicators for the future direction of engineering microorganisms as plastic cell factories. On the basis of our current understanding of PHA biosynthesis systems, we discuss recent advances in the approaches adopted for strain development in the production of non-natural polyesters, notably 2-hydroxycarboxylic acid-containing polymers, with particular reference to systems metabolic engineering strategies.     

Microbial production of lactate-containing polyesters

Due to our increasing concerns on environmental problems and limited fossil resources, biobased production of chemicals and materials through biorefinery has been attracting much attention. Optimization of the metabolic performance of microorganisms, the key biocatalysts for the efficient production of the desired target bioproducts, has been achieved by metabolic engineering. Metabolic engineering allowed more efficient production of polyhydroxyalkanoates, a family of microbial polyesters. More recently, non-natural polyesters containing lactate as a monomer have also been produced by one-step fermentation of engineered bacteria. Systems metabolic engineering integrating traditional metabolic engineering with systems biology, synthetic biology, protein/enzyme engineering through directed evolution and structural design, and evolutionary engineering, enabled microorganisms to efficiently produce natural and non-natural products. Here, we review the strategies for the metabolic engineering of microorganisms for the in vivo biosynthesis of lactate-containing polyesters and for the optimization of whole cell metabolism to efficiently produce lactate-containing polyesters. Also, major problems to be solved to further enhance the production of lactate-containing polyesters are discussed.     

微生物耐受乙醇与丁醇机制及其在生物燃料生产与生物转化中的应用

生物法获取乙醇与丁醇过程中有机溶剂的毒性是生产菌重要环境胁迫因素之一,且当有机溶剂超过一定浓度时便会抑制微生物的生长,甚至引起微生物的死亡,因此提高工业微生物的有机溶剂耐受性对工业生产具有重要的意义。对微生物乙醇及丁醇耐受机制的研究可为选育具有较强溶剂耐受菌提供理论基础。本文系统介绍了微生物耐受乙醇与丁醇的机制,并对其在生物燃料生产及生物转化中面临的机遇与挑战等问题进行简要的评述。     

Development of GRAS strains for nutraceutical production using systems and synthetic biology approaches: advances and prospects

Nutraceuticals are food substances with medical and health benefits for humans. Limited by complicated procedures, high cost, low yield, insufficient raw materials, resource waste, and environment pollution, chemical synthesis and extraction are being replaced by microbial synthesis of nutraceuticals. Many microbial strains that are generally regarded as safe (GRAS) have been identified and developed for the synthesis of nutraceuticals, and significant nutraceutical production by these strains has been achieved. In this review, we systematically summarize recent advances in nutraceutical research in terms of physiological effects on health, potential applications, drawbacks of traditional production processes, characteristics of production strains, and progress in microbial fermentation. Recent advances in systems and synthetic biology techniques have enabled comprehensive understanding of GRAS strains and its wider applications. Thus, these microbial strains are promising cell factories for the commercial production of nutraceuticals.     

New approaches to analyzing microbial biodiversity data

Modern molecular techniques have revealed an extraordinary diversity of microorganisms, most of which are as yet uncharacterized. This poses a major challenge to microbial ecologists: how can one compare the microbial diversity of different environments when the vast majority of microbial taxa are usually unknown? Three statistical approaches developed by ecologists and evolutionary biologists--parametric estimation, nonparametric estimation and community phylogenetics--are proving to be promising tools to meet this challenge. The combination of these tools with molecular biology techniques allow the rigorous estimation and comparison of microbial diversity in different environments.     

高通量测序技术在食品微生物研究中的应用

高通量测序技术的快速发展对食品微生物发酵过程和机制研究产生了深刻的影响,主要体现在食品微生物生理功能、代谢能力和进化的研究以及食品微生物群落结构、动态变化及其对环境的响应机制等方面。另外,通过对食品微生物基因组和元基因组进行数据分析,也对食品发酵过程优化、微生物功能改造、食源性微生物疾病预防和控制等提供了重要的依据。本文总结了近年来利用高通量测序技术对食品微生物基因组和元基因组进行测序的研究,并探讨了测序技术的发展对食品微生物研究的影响及发展趋势。     

生物热对传统固态发酵菌群演替及其代谢影响的研究进展

解析传统固态发酵中产生的生物热对微生物菌群代谢的影响,是认识发酵机制、调控发酵过程、保证发酵效率的关键之一。固态发酵过程中,微生物菌群代谢活动所产生的生物热及传热效率低等问题引起微环境温度升高,进而影响微生物的生长与代谢。然而,关于传统固态发酵微生物受生物热的影响及其适应机制仍不明晰。因此,本文以传统固态发酵体系为研究对象,阐述持续生物热介导的高温对固态发酵过程中微生物群落演替和代谢功能的影响,并提出复杂群落中具有多层次调控微生物代谢以适应高温环境的方式,主要从微生物群体与个体层面介绍可能存在的耐热机制。了解生物热对传统固态发酵微生物的影响及潜在的耐热机制,有助于靶向调控发酵过程、强化高温发酵等,以满足未来的工业化需求。     

油藏微生物及其压力适应机制

目前我国油田开发主要处于高含水后期,微生物驱提高石油采收率技术(MEOR)以低成本、环境友好等独特的优势引起了石油工业界的重视。实际上,经过半个多世纪的发展,MEOR已经成为提高采收率的重要前沿技术。高压是油藏的主要环境特征,在影响油藏微生物生存与活性等方面具有重要作用。本文从油藏及其微生物的主要特征、微生物对高压环境的适应机制以及高压下微生物降解烃的代谢特征等方面进行了综述。介绍了对油藏微生物资源、群落结构、微生物在油水相中分布的认识,微生物乳化原油机制,以及微生物在油藏厌氧环境中协同代谢、受温度和压力影响的特点,并列举了MEOR的矿场应用。在高压适应机制上,微生物主要通过改变和调整细胞膜结构、增加胞内脂质组分和表达胞内特殊酶等作用来实现对压力的适应;在高压下烃降解微生物代谢速率低于常压,而且耐压菌和嗜压菌具有不同的烃降解效率。