工业微生物酸胁迫的耐受机制及改造途径

工业微生物在发酵生产过程中会面对发酵环境和自身产生的各类酸性物质,而这些酸性物质会影响工业微生物的生长和代谢,即产生酸胁迫。微生物通过调控胞内质子浓度、保护和修复生物大分子、改变细胞膜组分以及整体水平调控等耐受机制来应对酸胁迫。结合酸胁迫的各种耐受机制,利用自然筛选和人工改造的方法提高工业微生物的抗酸胁迫能力,为构建出更能适应工业生产条件的菌株提供理论依据。     

TOR信号调控真菌细胞的生长与代谢

TOR(target of rapamycin)是一类进化上保守的丝氨酸/苏氨酸(Ser/Thr)蛋白激酶,是真核细胞响应环境信号调控生长和代谢的关键因子。真菌TOR信号途径在营养、压力环境等刺激下,通过核糖体生物合成、营养物质摄入及代谢等过程调节维持胞内稳态。本文主要综述了酵母细胞TOR及TOR复合物的结构,以及近年来真菌TORC1蛋白在不同营养环境、压力等条件下对细胞生长与自噬、代谢以及胁迫生理响应等生命活动的调控机制进展及未来发展方向,为真菌TOR调控生长和代谢产物提供新思路。     

Sigma因子高效调控微生物多功能研究进展

Sigma因子分为两大类,分别为σ~(70)家族和σ~(54)家族。σ~(70)家族的基础sigma因子,一般指导基因转录、应激反应、细胞发育以及辅助代谢,而σ54家族参与细菌的氮和碳水化合物代谢、生物膜形成等。近年来研究发现,宿主体内的sigma因子可通过调节基因表达来响应外界环境的改变、细胞发育信号以及指导生物代谢的合成;并且还发现原核生物有抗-sigma因子和抗-抗sigma因子存在。一些微生物体内的sigma70因子能调控其抗生素、激素或某些代谢产物的产生,指导细胞耐酸、耐高渗或耐高温等胁迫条件,还能增强微生物的生长能力;sigma54因子通常也能调节生物体代谢途径及氮源利用,参与生物固氮调控等。为了揭示sigma因子在高效调控生物多功能方面的研究成果,现对sigma因子及相关因子的结构特点、作用机制、生物多功能以及sigma因子调控固氮功能等方面进行阐述。     

ppGpp介导的抗生素胁迫应答机制研究进展

抗生素是由微生物在生长发育后期产生的次级代谢产物,具有杀死或抑制细菌生长的能力,因此被广泛应用于细菌感染的临床治疗。在长期的进化过程中,细菌采取多种方式应对环境中抗生素的威胁。除了广为人知的抗生素耐药性(resistance)之外,细菌还能对抗生素产生耐受性(tolerance)和持留性(persistence),严重影响抗生素的临床疗效。鸟苷四磷酸(guanosine tetraphosphate, ppGpp)和鸟苷五磷酸(guanosine pentaphosphate, pppGpp) (本文统称ppGpp)是细菌应对营养饥饿等不利环境时产生的"报警"信号分子,其能够在全局水平调控基因的表达,使细菌适应不利的环境。越来越多的研究表明,ppGpp与细菌应对抗生素胁迫密切相关。基于此,本文综述了细菌中ppGpp的合成与水解及其作用机制,并重点阐述了ppGpp介导抗生素胁迫应答的分子机制,以期为新型抗生素的开发提供新思路。     

细菌对胁迫应答因子RpoS的调控

RpoS是细菌一般胁迫反应的主要调控因子,可以诱导RpoS表达的胁迫条件包括碳源和氮源饥饿、渗透压升高、低pH、温度升高等。在细菌体内,大量环境和细胞内信号参与RpoS的调控。这些调控可以发生在转录和翻译水平、降解过程以及活性调节等方面,形成一个复杂的调控网络。RpoS调控机制的阐明对于了解胁迫条件下细菌响应机制具有重要意义。     

生物被膜在病原细菌与植物识别中的作用

生物被膜是微生物附着在生物或非生物表面所形成的一种三维结构,细胞被其自身所产生的胞外聚合物所包围,生物被膜的形成被认为是微生物应对生物和非生物胁迫时所产生的一种自我防御机制。众多微生物能够在植物叶、维管束和根等组织中生长,并在植物不同组织表面附着形成生物被膜,病原细菌的生物被膜随植物内部环境动态变化是其有效发挥致病作用的关键,研究植物病原细菌生物被膜调控机制是认识植物-病原菌互作的重要方面。文中将系统地介绍植物病原细菌生物被膜特征、组成成分、分子调控机制及最新研究进展。     

多聚磷酸盐在微生物抗环境胁迫中的作用及机制

抗环境胁迫是微生物提高环境适应性和增加生存机会的一个重要策略，探明微生物抗环境胁迫的过程及分子机制对于了解微生物进化和开发微生物资源具有重要意义。多聚磷酸盐（polyphosphate, polyP）在微生物抗环境胁迫中发挥重要作用。在营养限制条件下，polyP可充当微生物的能源来源和信号分子，增强微生物对低营养环境的适应能力。在微生物应对环境胁迫过程中，polyP可作为蛋白质的伴侣，通过蛋白质修饰改变蛋白质结构使其免受失活，从而维持其功能完整性。polyP具有金属螯合能力，可提高微生物对重金属胁迫的抵抗能力。微生物能通过调节polyP的合成来适应环境pH的改变，调节酸碱胁迫过程中的能量消耗。基于polyP抗环境胁迫的特性，通过转基因技术，把polyP合成相关基因转入到农作物中，可以增加农作物体内polyP含量，从而提高农作物抗环境胁迫的能力。利用含有polyP的微生物处理重金属废水，可极大地提高重金属离子的去除效率。同时，微生物中合成的polyP颗粒也能进一步开发为生物活性产品。因此，polyP在微生物抗胁迫中发挥多样化作用，通过各种分子途径提高微生物对环境胁迫的耐受性。加强poly...     

微生物硫代谢与抗逆性

硫代谢是微生物重要的生命代谢活动。微生物对外源硫酸盐的转运、同化、代谢调控以及重要含硫化合物的生物合成，不但与微生物生长代谢相关，而且影响微生物在胁迫环境下的抗逆性和鲁棒性。目前，大部分研究都聚焦在微生物硫酸盐同化过程和H₂S产生，对于微生物硫代谢与抗逆性相关的研究较少。本文总结了近年来微生物硫代谢过程中的硫酸盐转运、同化路径以及调控方式；并结合微生物在不同胁迫条件下的氧化应激反应，探讨了含硫化合物如硫化氢、谷胱甘肽和半胱氨酸等提高微生物抗逆性的机制。硫代谢与微生物抗逆性相关机制的解析不仅为理解微生物硫代谢与抗逆性提供理论基础，也为设计与构建抗逆性强的高产稳产工业菌株提供分子靶点。     

植物苯丙烷代谢途径

众所周知,固着生长的植物经常受到环境中各种生物和非生物胁迫的威胁。所以在漫长的进化过程中,植物必须将多样的环境信号整合到其发育过程中,以实现适应性形态的发生和代谢途径的精确调控,最终使植物完成整个生长周期。研究显示,苯丙烷代谢作为植物重要的次级代谢途径之一,其代谢产物,例如木质素、孢粉素、花青素和有机酸等,在调控植物适应性生长的过程中发挥着重要功能。特别是在药用植物中,苯丙烷代谢还与众多药用活性成分的合成息息相关,几乎所有包含苯丙烷骨架的天然药效成分均由苯丙烷代谢途径直接或间接合成,例如黄酮类、萜类和酚类等。此外,经苯丙烷代谢途径产生的一些次级代谢产物还能由植物根系外泌到周际土壤中,通过改变根系微生物的菌群生态,而影响植物生长和抵抗生物或非生物胁迫的能力。同时,苯丙烷代谢介导的这种植物-微生物互作也与药用植物的道地品质密不可分。本文综述了近年来植物苯丙烷代谢途径的最新研究进展,重点对该代谢途径中代谢产物的生理功能及表达调控机制进行了介绍,以期更深入地理解药用植物苯丙烷代谢与药材性状之间的潜在关系,旨在指导优良中草药的遗传育种,以进一步促进我国中医药事业的蓬勃发展。     

RNA-Seq揭示Foc4在外源氧化胁迫(H_2O_2)下的基因表达及细胞代谢变化

尖孢镰刀菌古巴专化型4号小种(Fusarium oxysporum f. sp. cubense race 4,Foc4)是香蕉枯萎病的强致病性病原菌。Foc4在侵染香蕉植株早期必须面对寄主的活性氧迸发。【目的】了解Foc4应对外源氧化胁迫的分子机制。【方法】利用Illumina 2500 RNA-Seq测序平台分析了经外源氧化胁迫(H_2O_2)处理的Foc4与对照在转录组水平的基因表达差异。【结果】在外源氧化胁迫条件下,Foc4的生长受到抑制。转录组测序获得了超过2千万条clean reads。进一步的差异基因表达分析以差异倍数FC (fold change)≥2且FDA值≤0.001为选择标准,发现496个基因表达上调,298个基因表达下调。GO功能富集分析显示,429个基因比对到GO功能分析数据库,在这些差异表达基因中,许多与代谢过程、生物调节、细胞过程和刺激应答有关。KEGG通路富集分析显示,有141个表达差异显著基因比对到KEGG中的50条代谢途径。其中,主要是各类氨基酸代谢途径、脂肪酸代谢途径。同时也包括与抗氧化胁迫直接相关的代谢途径,包括DNA的损伤修复、类胡萝卜素的生物合成、过氧化物酶体、谷胱甘肽代谢等。【结论】这些结果暗示,为了在强氧化胁迫环境下生存,Foc4细胞从包括直接应对氧化胁迫的信号调控途径在内的物质代谢和能量代谢均发生改变以应对环境变化的胁迫。     

Nitrogen-fixing bacteria alleviates competition between arbuscular mycorrhizal fungi and Solidago canadensis for nutrients under nitrogen limitation

丛枝菌根真菌(AMF)能与大多数陆生植物的根系形成共生体, 有助于宿主植物吸收养分。但营养胁迫下, 根系微生物对AMF与宿主植物间关系的影响少见报道。该研究假设: 在营养极度匮乏(如氮胁迫)环境下, AMF与宿主植物可能产生营养竞争, 而固氮菌的介入能够缓解两者对营养的竞争关系。为了验证这一假设, 该文探究了加拿大一枝黄花(Solidago canadensis)生长受限的氮浓度, 并在氮受限条件下检验了AMF、加拿大一枝黄花及固氮菌三者间的关系。结果表明: 低氮处理明显抑制了加拿大一枝黄花的地上生物量和总生物量, 尤其以0.025 mmol·L^-1 N的氨态氮对加拿大一枝黄花的负影响更甚。在此氮浓度下, 单独添加AMF总体上都进一步抑制了加拿大一枝黄花的生长, 而固氮菌的添加在一定程度上提高了氮受限条件下AMF对宿主的根部侵染率及宿主植物生物量。这表明固氮菌能够缓和氮受限条件下AMF和加拿大一枝黄花间的营养竞争关系。研究结果加深了对外来植物在极度营养胁迫环境下与多种微生物互作的入侵机制的理解。     

固氮菌缓解氮限制环境中丛枝菌根真菌对加拿大一枝黄花的营养竞争

丛枝菌根真菌(AMF)能与大多数陆生植物的根系形成共生体, 有助于宿主植物吸收养分。但营养胁迫下, 根系微生物对AMF与宿主植物间关系的影响少见报道。该研究假设: 在营养极度匮乏(如氮胁迫)环境下, AMF与宿主植物可能产生营养竞争, 而固氮菌的介入能够缓解两者对营养的竞争关系。为了验证这一假设, 该文探究了加拿大一枝黄花(Solidago canadensis)生长受限的氮浓度, 并在氮受限条件下检验了AMF、加拿大一枝黄花及固氮菌三者间的关系。结果表明: 低氮处理明显抑制了加拿大一枝黄花的地上生物量和总生物量, 尤其以0.025 mmol·L^-1 N的氨态氮对加拿大一枝黄花的负影响更甚。在此氮浓度下, 单独添加AMF总体上都进一步抑制了加拿大一枝黄花的生长, 而固氮菌的添加在一定程度上提高了氮受限条件下AMF对宿主的根部侵染率及宿主植物生物量。这表明固氮菌能够缓和氮受限条件下AMF和加拿大一枝黄花间的营养竞争关系。研究结果加深了对外来植物在极度营养胁迫环境下与多种微生物互作的入侵机制的理解。     

On multiple-nutrient-limited growth of microorganisms,with special reference to dual limitation by carbon and nitrogen substrates

Simultaneous limitation of microbial growth by two or more nutrients is discussed for dual carbon/nitrogen-limited growth in continuous culture. The boundaries of the zone where double-limited growth occurs can be clearly defined from both cultivation data and cellular composition and they can be also predicted from growth yield data measured under single-substrate-limited conditions. It is demonstrated that for the two nutrients carbon and nitrogen the zone of double nutrient limitation is dependent on both the C:N ratio of the growth medium and the growth (dilution) rate. The concept on double-(carbon/nitrogen)-limited growth presented here can be extended to other binary and multiple combinations of nutrients.     

Soil parent material—A major driver of plant nutrient limitations in terrestrial ecosystems

Because the capability of terrestrial ecosystems to fix carbon is constrained by nutrient availability, understanding how nutrients limit plant growth is a key contemporary question. However, what drives nutrient limitations at global scale remains to be clarified. Using global data on plant growth, plant nutritive status, and soil fertility, we investigated to which extent soil parent materials explain nutrient limitations. We found that N limitation was not linked to soil parent materials, but was best explained by climate: ecosystems under harsh (i.e., cold and or dry) climates were more N‐limited than ecosystems under more favourable climates. Contrary to N limitation, P limitation was not driven by climate, but by soil parent materials. The influence of soil parent materials was the result of the tight link between actual P pools of soils and physical–chemical properties (acidity, P richness) of soil parent materials. Some other ground‐related factors (i.e., soil weathering stage, landform) had a noticeable influence on P limitation, but their role appeared to be relatively smaller than that of geology. The relative importance of N limitation versus P limitation was explained by a combination of climate and soil parent material: at global scale, N limitation became prominent with increasing climatic constraints, but this global trend was modulated at lower scales by the effect of parent materials on P limitation, particularly under climates favourable to biological activity. As compared with soil parent materials, atmospheric deposition had only a weak influence on the global distribution of actual nutrient limitation. Our work advances our understanding of the distribution of nutrient limitation at global scale. In particular, it stresses the need to take soil parent materials into account when investigating plant growth response to environment changes.     

氮添加诱导的磷限制改变了亚热带黄山松林土壤微生物群落结构

土壤微生物在陆地生态系统的生物地球化学循环中起着重要作用。然而目前尚不清楚氮(N)添加量及其持续时间如何影响土壤微生物群落结构,以及微生物群落结构变化与微生物相对养分限制状况是否存在关联。本研究在亚热带黄山松林开展了N添加试验以模拟N沉降,并设置3个处理:对照(CK, 0 kg N·hm^-2·a^-1)、低N(LN, 40 kg N·hm^-2·a^-1)和高N(HN, 80 kg N·hm^-2·a^-1)。在N添加满1年和3年时测定土壤基本理化性质、磷脂脂肪酸含量和碳(C)、N、磷(P)获取酶活性,并通过生态酶化学计量分析土壤微生物的相对养分限制状况。结果表明: 1年N添加对土壤微生物群落结构无显著影响,3年LN处理显著提高了革兰氏阳性菌(G⁺)、革兰氏阴性菌(G^-)、放线菌(ACT)和总磷脂脂肪酸(TPLFA)含量,而3年HN处理对微生物的影响不显著,表明细菌和ACT对N添加可能更为敏感。N添加加剧了微生物C和P限制,而P限制是土壤微生物群落结构变化的最佳解释因子。这表明,N添加诱导的P限制可能更有利于部分贫营养菌(如G⁺)和参与P循环的微生物(如ACT)的生长,从而改变亚热带黄山松林土壤微生物群落结构。     

Cheaters, diffusion and nutrients constrain decomposition by microbial enzymes in spatially structured environments

Extracellular enzymes allow microbes to acquire carbon and nutrients from complex molecules and catalyse the rate-limiting step in nutrient mineralization. Because the factors regulating enzyme production are poorly understood, I used a simulation model to examine how competition, nutrient availability and spatial structure affect microbial growth and enzyme synthesis. In simulations where enzyme-producing microbes competed with cheaters (who do not synthesize enzymes but take-up product), higher enzyme costs favoured cheaters, while lower rates of enzyme diffusion favoured producers. Cheaters and producers coexisted in highly organized spatial patterns at intermediate enzyme costs and diffusion rates. Simulations with varying nutrient inputs showed that nitrogen supply can limit carbon mineralization, microbial growth and enzyme production because of the nitrogen-demanding stoichiometry of enzymes (C : N =  c. 3.5 : 1). These results suggest that competition from cheaters, slow diffusion and nitrogen limitation may constrain microbial foraging and the enzymatic decomposition of complex compounds in natural environments.     

Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.     

The influence of mesozooplankton on phytoplankton nutrient limitation: a mesocosm study with northeast Atlantic plankton

We used marine phytoplankton from mesocosms seeded with different zooplankton densities to study the impact of mesozooplankton on phytoplankton nutrient limitation. After 7 d of grazing (copepod mesocosms) or 9 d (appendicularian mesocosms) phytoplankton nutrient limitation was studied by enrichment bioassays. After removal of mesozooplankton, bioassay bottles received either no nutrients, phosphorus or nitrogen alone, or a combination of nitrogen and phosphorus and were incubated for 2 d. Phytoplankton reproductive rates in the bottles without nutrient addition were calculated after correction for grazing by ciliates and indicated increasing nitrogen limitation with increasing copepod abundance. No nutrient limitation was found in the appendicularian mesocosms. The increase of nutrient limitation with increasing copepod density seems to be mainly the result of a trophic cascade effect: Copepods released nanoplankton from ciliate grazing pressure, and thereby enhanced nitrogen exhaustion by nanophytoplankton and reduced nitrogen excretion by ciliates. Nitrogen sequestration in copepod biomass, the mechanism predicted by the ecological stoichiometry theory, seems to have been a weaker effect because there was only little copepod growth during the experiment.     

土壤酶计量揭示了武夷山黄山松林土壤微生物沿海拔梯度的碳磷限制变化

了解土壤胞外酶活性和酶计量的变化对评估山地生态系统土壤养分有效性和微生物的营养限制状况具有重要意义.然而,亚热带山地森林土壤微生物的营养限制状况对海拔梯度变化的响应及其驱动因素尚不清楚.本研究以武夷山不同海拔(1200～2000 m)黄山松林为对象,测定了土壤基本性质、微生物生物量以及与碳(C)、氮(N)、磷(P)循环...