西南地区高山湖泊中可培养细菌多样性及其所产胞外活性物质的特性

【目的】研究西南不同地区的高山湖泊中可培养细菌的多样性及其产胞外蛋白酶、纤维素酶和胞外多糖的能力。【方法】以西南4个不同地区的高山湖泊:雷波的马湖(LB)、中缅边境的凯邦亚湖(ZM)、沙德的莲花湖(SD)、腾冲的青海湖(TC)的水样为研究对象,利用稀释涂布平板方法对可培养细菌进行分离筛选,然后通过对可培养细菌的生理生化指标和16S r RNA基因序列进行分析,初步确定细菌属别;对分离得到的菌株进行产胞外蛋白酶和纤维素酶活性测定和产胞外多糖能力检测。【结果】从西南地区4个湖泊中共分离筛选得到41株细菌,其中LB 15株、ZM 13株、SD 7株、TC 6株。根据16S r RNA基因序列的系统进化分析,4个地区可培养细菌的组成和丰度存在明显差异,其中LB和ZM的优势菌属是芽孢杆菌属(Bacillus),其次是气单胞菌属(Aeromonas)和假单胞菌属(Pseudomonas),分离的TC菌株全部属于芽孢杆菌属(Bacillus),分离的SD菌株特异性较强。进一步酶活性和胞外多糖检测表明,分离得到的41株细菌中有28株菌的发酵产物具有蛋白酶活性,6株具有纤维素酶活性,17株可产胞外多糖(Exopolysaccharides,EPS)。其中有2株细菌同时产蛋白酶、纤维素酶和胞外多糖,10株细菌同时产蛋白酶和胞外多糖,2株细菌同时产蛋白酶和纤维素酶,1株细菌同时产纤维素酶和胞外多糖。【结论】西南4个高山湖泊中存在丰富的微生物菌种资源,且4个湖泊中筛选的可培养细菌受所处环境的影响大。其中莲花湖由于高海拔和较偏僻等特点,人为干扰小,分离得到的细菌类群与其他湖泊相比明显不同;而马湖、凯邦亚湖和青海湖3个湖泊的海拔相对较低,受人类活动影响较大,分离得到的细菌均较常见。此外高山湖泊中的可培养细菌具有分泌多种胞外活性物质特性,为工业化应用奠定了资源基础,极具更深入的开发和研究价值。     

北黄海沉积物可培养产蛋白酶细菌分离鉴定

【目的】揭示北黄海沉积物中可培养产胞外蛋白酶细菌及蛋白酶多样性,增加人们对北黄海生态系统中产蛋白酶菌多样性的认识,为海洋产蛋白酶微生物的挖掘提供菌群资源。【方法】分别将5个北黄海沉积物样品梯度稀释涂布至酪蛋白明胶筛选平板,选择性分离产蛋白酶细菌;并通过分析基于16S rRNA基因序列的系统发育关系,揭示这些细菌的分类地位和遗传多样性;分别测定胞外蛋白酶活性并对酶活较高的39株菌进行基于苯甲基磺酰氟(PMSF,丝氨酸蛋白酶抑制剂)、邻菲罗啉(o-phenanthroline,O-P,金属蛋白酶抑制剂)、E-64(半胱氨酸蛋白酶抑制剂)和pepstatin A(天冬氨酸蛋白酶抑制剂)4种抑制剂的酶活抑制实验以及所有菌株对3种底物(酪蛋白、明胶、弹性蛋白)的水解能力;分析这些细菌所产胞外蛋白酶的特性及多样性。【结果】从5个北黄海沉积物样品中分离获得66株产蛋白酶细菌,这些菌株隶属于Bacteroidetes、Proteobacteria、Actinobacteria和Firmicutes 4个门的7个属,其中Pseudoalteromonas(69.9%)、Sulfitobacter(12.1%)和Salegentibacter(10.6%)是优势菌群;沉积物中可培养的产蛋白酶细菌的丰度为104 CFU/g;蛋白酶酶活抑制实验表明所有测定菌株产生的胞外蛋白酶属于丝氨酸蛋白酶和/或金属蛋白酶,仅有少数菌株所产蛋白酶具有半胱氨酸蛋白酶或天冬氨酸蛋白酶活性。【结论】北黄海沉积物中可培养产蛋白酶细菌类群较为丰富,Pseudoalteromonas、Sulfitobacter和Salegentibacter菌株是优势菌群,测定菌株所产胞外蛋白酶主要是丝氨酸蛋白酶和/或金属蛋白酶。     

小菌虫肠道可培养细菌的分离鉴定 及产消化酶活性分析

摘要：目的 分离小菌虫肠道可培养细菌,并研究其产消化酶活性,探讨肠道细菌对小菌虫消化食物的影响。方法 采用传统细菌分离培养方法分离小菌虫肠道细菌,利用16S rDNA序列进行细菌分子鉴定;利用筛选培养基鉴别各细菌的产蛋白酶、脂肪酶、淀粉酶和纤维素酶活性。结果 在小菌虫肠道中分离到4种可培养细菌,分别是枯草芽胞杆菌（Bacillus subtilis）、肺炎克雷伯菌（Klebsiella pneumoniae）、Pseudocitrobacter faecalis和芽胞杆菌（Bacillus sp.）。其中,2种芽胞杆菌属细菌有产消化酶活性。枯草芽胞杆菌有产纤维素酶、淀粉酶和蛋白酶活性;芽胞杆菌仅有产蛋白酶活性,但产酶能力低于枯草芽胞杆菌。结论 小菌虫肠道细菌中可培养细菌结构简单,但其中的芽胞杆菌属细菌有产纤维素酶、淀粉酶和蛋白酶能力,说明小菌虫肠道中的2种芽胞杆菌属细菌可能有协助小菌虫进行食物消化的功能。     

1株金黄杆菌分离、鉴定及其胞外蛋白酶活性的初步研究

从无指盘臭蛙(Odorrana grahami)皮肤表面分离到1株具有胞外蛋白水解酶活性的菌株,命名为CW-E2T。初步研究发现CW-E2T系革兰阴性,菌体短杆状,无鞭毛,菌落呈圆形,边缘光滑并相互粘连,表面突起,产生黄色素,有金黄色光泽细菌。通过形态学、生理生化和16SrRNA基因序列分析,确定CW-E2T为金黄杆菌属内的一个未定种。在此基础上对该菌株蛋白水解酶进行了初步研究,确定菌株CW-E2T胞外蛋白酶为金属蛋白酶。以上对CW-E2T细菌分类学研究和胞外蛋白酶的初步研究,为该菌株的大量培养以及胞外蛋白酶的进一步研究提供理论依据。     

木质纤维素的微生物降解

木质纤维素广泛存在于自然界中,因结构复杂,其高效降解需要多种微生物的协同互作,由于参与木质纤维素降解的微生物种类繁多,其协同降解机理尚不完全明确。随着微生物分子生物学和组学技术的快速发展,将为微生物协同降解木质纤维素机制的研究提供新的方法和思路。笔者前期研究发现,细菌复合菌系在50℃下表现出强大的木质纤维素降解能力,菌系由可分离培养和暂时不可分离培养细菌组成,但是可分离培养细菌没有降解能力。通过宏基因组和宏转录组研究表明,与木质纤维素降解相关的某些基因表达量发生显著变化,通过组学方法有可能更加深入解释微生物协同降解木质纤维素的微生物学和酶学机理。文中从酶、纯培养菌株和复合菌群三个方面综述了木质纤维素微生物降解研究进展,着重介绍了组学技术在解析复合菌群作用机理方面的现状和应用前景,以期为探索微生物群落协同降解木质纤维素的机理提供借鉴。     

粘细菌基因组学研究进展

粘细菌(Myxobacteria)隶属于δ变形菌纲(Deltaproteobacteria)的粘球菌目(Myxococcales),是一类革兰氏阴性杆状细菌。它是继放线菌和真菌之后又一重要的活性次级代谢产物产生菌,尽管如此,由于分离纯化困难,粘细菌的研究进展一直较为缓慢。随着测序技术的进步和生物信息学的应用,大量粘细菌基因组被完成测序和报道。本文对粘细菌研究意义及该类资源开发价值、分离培养存在的困难进行了阐述,对粘细菌基因组注释及目前已测菌株的全基因组进行了归纳总结,同时介绍了基因组学在粘细菌生态、捕食机制、子实体形成以及次级代谢产物合成方面的研究进展。本文有助于了解基因组学在粘细菌研究中的重要价值,为联合应用多组学技术深入研究粘细菌代谢机制和社会性行为提供了参考,对粘细菌基础研究、资源发掘和开发利用具有重要意义。     

马里亚纳海沟不同深度水样微生物分离与多样性分析

【背景】马里亚纳海沟挑战者深渊是地球表面最深点,认识其微生物群落结构和分离培养的微生物对挖掘新的微生物资源具有重要意义。【目的】对马里亚纳海沟不同深度水样进行细菌分离培养,并与这些样品的微生物群落结构进行比较,认识进一步要分离培养的微生物类型。【方法】采用不同培养基对马里亚纳海沟两个站位不同深度水样进行细菌分离培养,并通过Illumina MiSeq高通量测序分析各个水样的细菌和古菌的群落结构。【结果】从来自两个站位不同深度的6个水样样品中分离获得783株细菌,属于4个门6个纲28个属。其中,变形菌门占主导地位,67.8%的菌株属于γ-变形菌纲。分离获得的菌株主要属于亚硫杆菌属、假单胞菌属和交替假单胞菌属,它们在这些样品中广泛分布,且在高通量测序结果中也能检测到。高通量测序结果表明除浅层样品优势微生物为蓝细菌外,其他样品以变形菌门占主导;不同深度样品的微生物群落结构存在较大差异。【结论】马里亚纳海沟不同深度水样中不仅分离培养出了相对丰度较高的一些细菌属,也分离得到一些相对丰度较低的微生物类型。从马里亚纳海沟水样中分离培养获得的细菌菌株资源将用于功能微生物和功能酶挖掘等相关研究,这有利于...     

平板混合培养木质纤维素降解菌研究进展

微生物的混合培养已广泛应用于木质纤维素类物质的转化与降解领域.不同木质纤维素降解菌在混合培养时的相互关系在很大程度上影响混合培养的效果.目前对这种相互关系的研究主要依托平板混合培养展开,所用到的平板主要有基础培养基平板和改进培养基平板两种.其中基础培养基平板法主要根据菌落形态、菌丝体颜色、胞外挥发性有机化合物成分和典型胞外酶活性等进行研究,而改进培养基平板则是将基础培养基平板中的碳源更换为天然木质纤维素类物质进行对比研究.本文综述了采用平板混合培养不同木质纤维素降解菌菌株的研究现状和进展,并对该领域研究应重点关注的问题进行了展望.     

基于细菌共现网络的土壤粘细菌分离

粘细菌是一类分布广泛的捕食性细菌,能够产生种类多样、结构新颖、作用机制独特的天然活性物质。但是粘细菌分离纯化困难且耗时,导致其资源匮乏,这已成为粘细菌开发利用的重要瓶颈之一。基于辅助菌的分离方法是当前获得粘细菌资源的重要方法,然而辅助菌多为大肠杆菌（Escherichia coli）等革兰氏阴性菌。为了获得新的辅助菌和粘细菌资源,本研究基于土壤细菌16S rRNA基因高通量测序数据构建细菌共现网络（bacterial co-occurrence network）,发现粘细菌-细菌子网络中有27%的连接节点为放线菌。因此,本研究选择革兰氏阳性菌球形节杆菌（Arthrobacter globiformis） GDMCC 1.1730作为辅助菌,并在捕食培养基上验证其捕食活性。结果表明该辅助菌能够被所有参与测试的粘细菌（12个物种）所捕食。以GDMCC 1.1730作为辅助菌进行粘细菌的分离,共诱导出11种粘细菌子实体,且包括一种仅由GDMCC 1.1730诱导而大肠杆菌未能诱导出的子实体。本研究基于细菌共现网络和捕食活性验证,提供了一株革兰氏阳性菌作为新的粘细菌辅助菌,该辅助菌能够诱导出土壤中的多种粘细菌子实体,为根据细菌共现网络获取未/难培养微生物资源提供了新的证据。     

广东南岭森林土壤中可培养细菌多样性

广东南岭森林土壤中蕴藏着丰富的生物资源,但对其中的可培养细菌种类仍缺乏系统了解。本研究采用贫营养型的R2A培养基和富营养型的TSA培养基对南岭森林土壤中细菌进行了分离,获得细菌408株,分别从属于厚壁菌门、变形菌门、放线菌门和拟杆菌门的35属。其中的优势类群为厚壁菌门,占分离总数量的71%。在属水平,芽胞杆菌及其近缘属为优势类群。除芽胞杆菌外,假单胞菌、伯克霍尔德氏菌、草酸杆菌科Collimonas属和罗丹诺杆菌科Dyella属是分离获得的主要类群。R2A培养基在分离革兰氏阴性的变形菌门菌株方面表现出一定的偏好性,而TSA培养基分离得到的更多为快速生长的芽胞杆菌及其近缘的革兰氏阳性细菌。发现了15属的菌株具有一定的水解酶活性,大多表现出对淀粉和牛奶的水解活性,对有机磷的水解性能优于对无机磷的水解。降解纤维素的菌株则主要集中于芽胞杆菌及其近缘属中。发现了潜在新物种26株,分布于芽胞杆菌、Dyella、类芽孢杆菌等9属中。本研究仅使用了两种营养类型的培养基,进一步借助培养组学技术有望能更加全面反映南岭森林土壤中的可培养微生物多样性。     

粘细菌资源挖掘与多相分类研究进展

粘细菌(Myxobacteria)是一类具有复杂多细胞行为、能够广泛捕食各类细菌和真菌并能产生丰富次级代谢产物的药源微生物,具有重要研究和应用价值。然而,由于资源挖掘困难,多相分类研究进展缓慢,严重阻碍了粘细菌的开发利用。本文对粘细菌的特性、分离和纯化方法、目前存在的不足及改进措施进行阐述,并对粘细菌多相分类研究进展及存在的问题进行解析。另外,结合当前技术手段和发展现状,进一步对粘细菌的未来发展趋势进行展望,以期为相关研究提供参考。     

Myxobacteria isolated in Israel as potential source of new anti-infectives

AIMS: To evaluate the patterns of the production of antimicrobial compounds by Israeli myxobacteria newly isolated from soil samples and barks by a battery of isolation and purification methods. METHODS AND RESULTS: A total of 100 myxobacteria belonging to five of the 12 described genera, were isolated from 48 soil and 45 tree bark samples collected in different areas inside the State of Israel. Four isolation methods based on the peculiar metabolic and cell cycle aspects of myxobacteria, were combined with purification procedures and optimization of cultivation conditions. Ninety-seven strains were fermented and screened for antimicrobial activities. Production of antimicrobial activities was detected in 62 isolates. More than 50% of the collection (54 strains) was able to inhibit Escherichia coli growth. CONCLUSIONS: The results of this study support the idea that myxobacterial strains can be isolated from particular habitats and then cultivated and screened for their capacity to produce secondary metabolites endowed with antibacterial and antifungal activities. Myxovirescin, a typical poliketide myxobacterial antibiotic, has been identified in one Israeli isolate. Althiomycin, a thiazolyl peptide, which inhibits prokaryotic protein synthesis, usually produced by actinomycetes, was detected in three strains selected in this study. SIGNIFICANCE AND IMPACT OF THE STUDY: The results confirm that myxobacteria are prolific producers of a variety of bioactive secondary metabolites including antibacterial and antifungal compounds, being their high frequency of anti-Gram-negative activities particularly appealing for the current anti-infective research. So far their screening has often been hampered because their isolation is time-consuming and are quite difficult to handle and cultivate. In this paper we demonstrate that a proper combination of isolation, purification and cultivation methods allow their pharmaceutical exploitation.     

Fruiting and non-fruiting myxobacteria: a phylogenetic perspective of cultured and uncultured members of this group

The diversity of myxobacteria present in campus garden soil was surveyed by both cultivation-based and cultivation-independent methods. Detailed phylogenetic analysis of cultured and uncultured myxobacteria 16S rRNA gene sequences revealed that many undescribed relatives of the myxobacteria exist in nature. Molecular systematic analyses also revealed that myxobacterial genera described to date on the basis of the morphology of multi-cellular fruiting bodies were mostly monophyletic. However, these known taxa comprised only in a small part of the sequences recovered directly from soil in a cultivation-independent approach, indicating that the group is much more diverse than previously thought. We propose that the myxobacteria exist in two forms: the fruiting and the non-fruiting types. Most of the uncultured myxobacteria may represent taxa which rarely form fruiting bodies, or may lack some or all of the developmental genes needed for fruiting body formation. In order to identify non-fruiting myxobacteria, new morphology-independent cultivation and isolation techniques need to be developed.     

嗜盐古菌几种常见胞外酶研究进展

嗜盐古菌是一类生活于极端高盐环境的化能异养型原核微生物,其所分泌的胞外酶(外泌酶)具有在高盐条件下仍能保持活性的特点,在制革工业、高盐有机废水处理和泡菜加工等腌制食品方面发挥重要用途。本文对嗜盐古菌的胞外蛋白酶、淀粉酶、酯酶等几种常见胞外酶的来源和基本酶学性质的最新研究进展进行综述,为更好地开发利用嗜盐古菌胞外酶资源提供参考。     

Improved methods of isolation and purification of myxobacteria and development of fruiting body formation of two strains

By using baiting techniques and different purification methods, a high number of myxobacterial strains have been isolated as pure cultures from soil of different regions of China. Because myxobacterial cells do not disperse easily in liquid media, a medium containing an enzymatic hydrolysate of casein (CEH) medium have been used for purification and purity tests combined in a single step. The key method, in which isolates are reintroduced to sterile rabbit dung to induce fruiting bodies formation, facilitates purification of myxobacteria. Sterile rabbit dung pellets are used to mimic the natural growth substance of these organisms which has the advantage that characteristic fruiting bodies emerge, which is a key characteristics in the taxonomy of myxobacteria. In this study, the optimum program of isolation and purification of some myxobacteria strains has been established which will facilitate screening programs. Moreover, the development of fruiting body formation of strain BD20 (Chondromyces) and strain BD54 (Cystobacter) have been recorded in this study.     

未培养环境微生物培养方法的研究进展

自然界中微生物种类繁多、功能多样、分布广泛,对人类健康安全、生态稳定和物种进化等发挥不可替代的作用.尽管微生物培养技术至今已有一百多年,然而由于各种限制因素的制约,目前成功分离培养的微生物仅占0.1％-1.0％,自然界中仍有十分丰富的微生物资源有待挖掘和开发利用.如何理解难培养微生物的制约因素并探索作用机制,同时借此开...     

Cold-adapted enzymes produced by fungi from terrestrial and marine Antarctic environments

Antarctica is the coldest, windiest, and driest continent on Earth. In this sense, microorganisms that inhabit Antarctica environments have to be adapted to harsh conditions. Fungal strains affiliated with Ascomycota and Basidiomycota phyla have been recovered from terrestrial and marine Antarctic samples. They have been used for the bioprospecting of molecules, such as enzymes. Many reports have shown that these microorganisms produce cold-adapted enzymes at low or mild temperatures, including hydrolases (e.g. α-amylase, cellulase, chitinase, glucosidase, invertase, lipase, pectinase, phytase, protease, subtilase, tannase, and xylanase) and oxidoreductases (laccase and superoxide dismutase). Most of these enzymes are extracellular and their production in the laboratory has been carried out mainly under submerged culture conditions. Several studies showed that the cold-adapted enzymes exhibit a wide range in optimal pH (1.0–9.0) and temperature (10.0–70.0?°C). A myriad of methods have been applied for cold-adapted enzyme purification, resulting in purification factors and yields ranging from 1.70 to 1568.00-fold and 0.60 to 86.20%, respectively. Additionally, some fungal cold-adapted enzymes have been cloned and expressed in host organisms. Considering the enzyme-producing ability of microorganisms and the properties of cold-adapted enzymes, fungi recovered from Antarctic environments could be a prolific genetic resource for biotechnological processes (industrial and environmental) carried out at low or mild temperatures.     

一株产纤维素酶细菌的筛选、鉴定及产酶条件优化

目的：筛选1株产纤维素酶的细菌。方法：通过对从腐烂朽木及其附近土壤中得到的样品进行富集培养、分离纯化得到16株纤维素分解菌,经刚果红染色鉴定和液体发酵培养后对其进行了菌种初步鉴定及产酶条件的初步优化。结果：获得1株纤维素酶分泌量较高的细菌LT3。结论：LT3为革兰氏阳性菌,菌体成杆状,经发酵优化培养后,较适产酶条件为甘蔗渣20g/L,pH7.0、30℃培养120h,CMC酶活为71.17U/mL,滤纸酶活为33.37U/mL。通过克隆其16S rDNA序列,对其进行系统进化分析,鉴定为蜡状芽孢杆菌。     

Modeling microbial dynamics in heterogeneous environments: growth on soil carbon sources

We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions in heterogeneous media such as soil and by the functional attributes of individual microbes. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20-μm size portions of the soil physical structure and in 111-μm size soil aggregates with a random pore structure. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences suggested different functional niches for these two microbe types in cellulose utilization. Our model predicted an emergent behavior in which co-existence of membrane-associated hydrolase and extracellular hydrolases releasing organisms led to higher cellulose utilization efficiency and reduced stochasticity. Our analysis indicated that their co-existence mutually benefits these organisms, where basal cellulose degradation activity by membrane-associated hydrolase-expressing cells shortened the soluble hydrolase buildup time and, when enzyme buildup allowed for cellulose degradation to be fast enough to sustain exponential growth, all the organisms in the community shared the soluble carbon product and grew together. Although pore geometry affected the kinetics of cellulose degradation, the patterns observed for the bacterial community dynamics in the 6-20 μm-sized micro-pores were relevant to the dynamics in the more complex 111-μm-sized porous soil aggregates, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied. As shown with examples in this study, various functional niches of the bacterial communities can be investigated using complex predictive mathematical models where the role of key environmental aspects such as the heterogeneous three-dimensional structure, functional niches of the community members, and environmental biochemical processes are directly connected to microbial metabolism and maintenance in an integrated model.