植物内生细菌的研究

植物内生细菌是能够定殖在植物细胞间隙或细胞内,并与寄主植物建立和谐联合关系的一类微生物I’］。自本世纪初开始,人们不断地从植物的根、叶、甚至茎和种子上分离并鉴定出多种微生物,但其在寄主植物中的生物学作用却未能引起研究者的重视。近年来,由于一些研究结果表明内生细菌能够作为外源基因的载体,又具有植物保护剂的功能,可以产生植物促生物质或可作为联合固氮菌剂,由此有关内生细菌的研究才引起植物学家和微生物学家的兴趣。l植物内生细菌的研究现状有关植物内生细菌的研究主要涉及两方面的内容：（l）生态学研究：内生细菌…     

植物内生微生物及其“暗物质”开发技术的研究进展

植物内生微生物包含内生菌、内生细菌、内生真菌、内生放线菌、内生古细菌等领域,其"暗物质"是指尚未被开发的菌种资源、遗传资源和代谢物资源。根据对宿主植物的作用,可以将内生微生物分为共生内生微生物、有益内生微生物和潜在的病原微生物三类。内生微生物在植物促生、提高植物抗逆性、提高植物的环境适应性、影响植物代谢物合成、参与被污染环境的修复等方面具有广泛的应用。具有生理活性的次级代谢产物的开发和利用是植物内生微生物研究的另一个热门领域,但由于大多数不能被分离培养、次级代谢物的分离分析技术不足等原因,使得大量的植物内生微生物资源仍处于未知状态。表面消毒技术、分离培养技术的改进,"多-组学"技术的联合使用和次级代谢物分离分析技术的发展极大促进了植物内生微生物的研究。在此基础上,开展微生物组研究和多单位多地域的协同研究将会进一步加快植物内生微生物资源的研究、发掘和利用。以上述内容为基础,本文综述了植物内生微生物的功能及其代谢产物研究进展,当前植物内生微生物研究的分离培养方法和组学技术,并在文章最后对该领域的研究方向提出了建议。     

兰科植物内生细菌物种多样性及其促生机理研究进展

内生细菌影响兰科植物菌根形成和共生关系的稳定性,在兰科植物的生活史中起着重要作用。内生细菌通过分泌植物激素、采用光合作用、生物固氮或促进矿质营养的循环以及产生铁载体、合成其他活性物质等途径来促进兰科植物生长发育。综述了兰科植物内生细菌物种多样性的研究方法及其对兰科植物的促生机理,基于兰科植物与共生微生物的密切关系,认为内生细菌间、内生细菌与兰科植物菌根真菌间的互作是揭示兰科植物与内生细菌互作机理的重要方向。     

植物内生菌的研究进展

植物内生菌是存在于植物内部与植物密不可分的一类微生物,包括内生真菌和内生细菌两大类。随着研究的不断深入,发现内生菌不仅产生多种有益的生物学作用,如防病、促生、固氮等,还能对寄主植物的生长发育产生不利影响。近年来,植物内生菌已成为我国微生物学领域研究的热点问题之一。本文综述了植物内生真菌和内生细菌的研究概况,以期更好地研究和了解植物内生菌。     

植物内生细菌测定方法的研究进展

伴随全功能体(holobiont)和全基因组(hologenome)概念的出现,植物微生物群落被看作植物全功能体的重要组成部分,其结构和功能逐渐得到研究和解析。内生细菌是植物微生物群落的成员之一,由于其定殖在组织内部而与宿主的接触更为紧密,因而其与植物的相互作用也更加直接、高效且不容易受到环境条件变化的影响。本文介绍了植物内生细菌的基本特点,并重点综述了植物内生细菌测定方法的国内外进展。了解内生细菌的基本特点并掌握其测定方法,将促进对内生细菌与植物互作机制的探索及对全功能体中内生细菌与宿主共生机理的解析,为植物的营养和抗病育种提供内生细菌角度的新策略。     

两种不同生境中国沙棘种子内生细菌的多样性

植物内生菌广泛分布于植物的各种组织及器官中,对植物的生长表现出各种作用,而植物种子中的内生菌对植物的作用也越来越受到人们的关注。以榆中县和秦安县两种不同生境的中国沙棘种子为材料,分析中国沙棘种子内生细菌多样性,以期探究生境对种子内生菌多样性的影响,并为进一步研究种子内生菌与沙棘的相互作用提供依据。研究利用纯培养方法和高通量测序方法分别进行中国沙棘种子内生细菌多样性分析。对纯培养分离得到的内生细菌,利用16S rRNA基因序列分析法结合形态学特征进行内生细菌的鉴定;对高通量测序得到的数据进行基于OTUs(Operational Taxonomic units,可操作分类单元)的物种注释分析。通过纯培养方法从榆中县中国沙棘种子中分离得到4株内生细菌,分属于芽孢杆菌属(Bacillus)、葡萄球菌属(Staphylococcus)和假单胞菌属(Pseudomonas);秦安县中国沙棘种子中分离得到5株内生细菌,分属于芽孢杆菌属(Bacillus)、葡萄球菌属(Staphylococcus)和不动杆菌属(Acinetobacter)。采用高通量测序方法检测到榆中县中国沙棘种子内生细菌分属于7个门、68个属,秦安县中国沙棘种子内生细菌分属于5个门、30个属。在门分类水平,榆中县中国沙棘种子内生细菌的主要优势门类是蓝藻门(Cyanobacteria)和变形菌门(Proteobacteria),相对丰度分别为95.62%和2.03%;秦安县中国沙棘种子的主要优势门类是变形菌门(Proteobacteria)和蓝藻门(Cyanobacteria),相对丰度分别为91.68%和8.06%。在属分类水平,榆中县中国沙棘种子内生细菌的优势菌属为蓝藻细菌属(Cyanobacteria),相对丰度为95.09%;秦安县中国沙棘种子内生细菌的优势菌属为寡养单胞菌属(Stenotrophomonas),相对丰度为85.60%。榆中县和秦安县两种不同生境中国沙棘种子内生细菌有着丰富的多样性,且内生细菌的多样性和丰富度存在明显差异,表现为榆中县中国沙棘种子内生细菌的多样性和丰富度均高于秦安县中国沙棘种子内生细菌。     

薄荷根内生及根际细菌多样性探究

采用传统的培养方法和基于分子生物学技术的非培养方法对我国常用中药之一的薄荷植物的根内生及根际细菌进行研究,从而了解其中细菌群落的多样性。对分离得到的细菌菌株进行16S rDNA扩增和系统发育分析,结果表明,利用培养方法与非培养方法分离得到薄荷根内生细菌及根际细菌一些共有的细菌种类,但前者优势种群为g-变形杆菌,后者优势种群为芽孢杆菌,说明土壤细菌,特别是根际细菌是植物内生细菌的重要来源,但植物对其内生细菌具有选择压。首次报道了薄荷根内和根际具有丰富的微生物群落多样性,为进一步探索植物根系微生态环境中微生物群落的形成和生态功能提供了基础信息。在今后探讨植物与微生物相互作用关系时,有必要考虑土壤环境,特别是根际对其的影响的同时,更加重视植物与其相关联的细菌种类的选择作用。     

植物内生细菌对植物健康的作用

植物内生菌是一个多样性十分丰富的微生物类群,存在于没有外在感染症状的健康植物组织内,并与宿主植物协同进化.随着研究领域的不断拓宽和研究方法的不断更新,植物内生菌与植物健康的关系以及应用逐渐成为研究热点.本文主要综述了内生细菌的多样性、进入植物组织内的机制以及内生细菌的主要功能及应用,提出了现阶段内生菌研究存在的问题,并展望了内生菌研究的前景.     

种子内生菌增强宿主植物重金属抗性的功能机制研究进展

种子是植物的繁殖器官,其内定殖有一定数量的内生菌,种子内生菌通过垂直传播成为新生植物组织内最早定殖的微生物,对连续几代植物内生菌群落的形成起着决定性作用,并在植物抗逆方面发挥着重要作用。本文对种子内生菌与宿主植物重金属抗性之间的关系及其功能机制进行综述,并对下一步研究方向予以展望。     

中国植物内生微生物研究的发展和展望

我国植物内生微生物的早期研究论文,基本上以非豆科植物根瘤菌Frankia属细菌为主。进入21世纪后,植物内生菌的研究,无论是研究领域的扩大,研究人员的增加,还是论文数量的递增都有了迅猛的发展,为国际上少有。我国植物内生微生物的研究具有资源探索多、分离培养多、活性检测多、活性物质功能研究多;方法研究少、涉及林木少、与宿主的关联少、实际应用少等特点。其研究主要集中在红豆杉类、红树类、鬼臼类、兰、银杏等植物中的内生微生物。论文的发表以药物开发为研究目标的最多,又以初级的资源探索型为最。以抗菌、抗肿瘤等指标为主的药物开发,是植物内生微生物研究中最耀眼的亮点,目前已获得了紫杉醇生产效率较高的内生真菌菌株资源。我国植物内生微生物研究有4大类24个应用研究的方向,其中特别值得关注的是豆科植物根瘤内生细菌的研究;尚待加强的有6个方面,尤其是深色有隔内生真菌(DSE)的研究。我国植物内生微生物研究在药用植物内生微生物的资源探索和筛选方面积累较丰富,而在有害内生微生物方面的研究则比较薄弱。最后,作者提示了一些尚待加强的研究技术,供相关人员参考。     

核心微生物组的研究及利用现状

随着分子生物学和生物信息学的飞速发展,新一代测序技术可以轻松地检测不同样本中复杂的微生物分类单元。面对这些复杂而大量的微生物组数据带来的分析挑战,利用核心微生物组的方法来描述和分析样本中的核心微生物组和关键种是近年来新的研究热点,这些结果将揭示与宿主健康、生长和生产等密切相关的微生物种类,有助于深入认识微生物与宿主间的相互关系,深刻理解微生物对宿主的影响作用,更好地理解微生物组在自然生态系统中的功能。本文阐述了核心微生物组的定义、研究方法、与动植物的关系等方面的研究及利用现状,为更好地利用核心微生物组解决环境、人类健康和农业生产问题提供思路。     

Community structure and diversity of endophytic bacteria in seeds of three consecutive generations of <Emphasis Type="Italic">Crotalaria pumila</Emphasis> growing on metal mine residues

Aims

We investigated the possible transgenerational transfer of bacterial seed endophytes across three consecutive seed generations of Crotalaria pumila growing on a metal mining site in Mexico.

Methods

Seeds were collected during three successive years in the semi-arid region of Zimapan, Mexico. Total communities of seed endophytes were investigated using DNA extraction from surface sterilized seeds and 454 pyrosequencing of the V5-V7 hypervariable regions of the 16S rRNA gene.

Results

The communities consisted of an average of 75 operational taxonomic units (OTUs); richness and diversity did not change across years. Methylobacterium, Staphylococcus, Corynebacterium, Propionibacterium and eight other OTUs constituted >60% of the community in each generation. The microbiome was dominated by Methylobacterium (present in >80% of samples). Functions associated with the microbiome were C and N fixation, oxidative phosphorylation and photosynthesis activity.

Conclusions

The bacterial endophytic communities were similar across three consecutive seed generations. Among the core microbiome Methylobacterium strains were the most abundant and they can contribute to nutrient acquisition, plant growth promotion and stress resilience to their host in metal contaminated mine residues. Identification of the seed microbiome of C. pumila may lead to novel and more efficient inoculants for microbe-assisted phytoremediation.

     

Spatial patterns of fungal endophytes in a subtropical montane rainforest of northern Taiwan

Fungal endophytes of plants are ubiquitous and important to host plant health. Wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across the Fushan forest dynamics plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Despite this, host tree species was an important predictor of mycobiome community-composition. Within a single common tree species, “core” mycobiomes were characterized using co-occurrence analysis. The spatial co-occurrence patterns of these few species of fungal endophytes appear to explain the strong host effect. For wood endophytes, a consistent core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.     

From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome

Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host–microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.     

一种自下而上的合成微生物组理性构建策略，用于郫县豆瓣发酵剂设计

【目的】提出一种合成微生物组的理性构建策略,用于构建郫县豆瓣蚕豆醅初始发酵的微生物组合菌剂。【方法】采取自下而上的合成微生物组理性构建策略,以相对丰度、频率和特征向量中心度作为核心微生物属的选择指标,分析确定蚕豆醅发酵核心微生物;设计模拟原位体系的全合成培养基,并利用该培养基快速、稳定地检测核心微生物包括产香性能在内的发酵特征。基于核心微生物的产香互补性能进行双菌组合发酵实验,结合核心微生物之间的生长相互作用,设计三菌组合发酵菌剂并验证其发酵性能。【结果】本研究确定并分离了郫县豆瓣蚕豆醅发酵过程中的 9种核心微生物。检测核心微生物产生的挥发性风味化合物,发现酵母菌类、乳酸菌类和其他类微生物之间存在产香互补关系。然后,结合微生物间的生长抑制关系设计了由乳酸片球菌、肉葡萄球菌及异变假丝酵母组成的三菌组合菌剂。与企业原位发酵样品相比,三菌组合菌剂产生的挥发性化合物数量达到原位样品的63.1%,化合物种类结构较为相似。与原位样品相比,组合菌剂样品氨基酸态氮浓度提升了21.8%。【结论】本研究提出了一种自下而上的合成微生物组理性构建策略,基于此策略设计了郫县豆瓣蚕豆醅发酵组合菌剂。使用该组合菌剂作为起始发酵剂发酵的郫县豆瓣蚕豆醅具有良好的风味谱和优异的氨基酸态氮水平。本研究在合成微生物组构建与发酵食品工艺改造方面具有较大的科学与应用价值。     

The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines

Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.     

Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown

Vertebrates harbour microbes both internally and externally, and collectively, these microorganisms (the ‘microbiome’) contain genes that outnumber the host's genetic information 10‐fold. The majority of the microorganisms associated with vertebrates are found within the gut, where they influence host physiology, immunity and development. The development of next‐generation sequencing has led to a surge in effort to characterize the microbiomes of various vertebrate hosts, a necessary first step to determine the functional role these communities play in host evolution or ecology. This shift away from a culture‐based microbiological approach, limited in taxonomic breadth, has resulted in the emergence of patterns suggesting a core vertebrate microbiome dominated by members of the bacterial phyla Bacteroidetes, Proteobacteria and Firmicutes. Still, there is a substantial variation in the methodology used to characterize the microbiome, from differences in sample type to issues of sampling captive or wild hosts, and the majority (>90%) of studies have characterized the microbiome of mammals, which represent just 8% of described vertebrate species. Here, we review the state of microbiome studies of nonmammalian vertebrates and provide a synthesis of emerging patterns in the microbiome of those organisms. We highlight the importance of collection methods, and the need for greater taxonomic sampling of natural rather than captive hosts, a shift in approach that is needed to draw ecologically and evolutionarily relevant inferences. Finally, we recommend future directions for vertebrate microbiome research, so that attempts can be made to determine the role that microbial communities play in vertebrate biology and evolution.     

植物内生菌生物抗菌活性物质研究进展

植物内生菌作为一种新型的微生物资源,分离和确定其代谢产物是一条寻找新型天然活性物质的重要途径。目前为止,许多研究者从不同的植物内生菌中分离到大量具有抗菌活性的新化合物,这些新的化合物被认为是解决日益严重的微生物多重耐药性的希望之一。本文从植物内生菌的多样性、抗菌活性物质多样性及国内内生菌研究进展等多个角度概述了当前有关植物内生菌研究的主要成果和最新进展,以期为植物内生菌相关研究提供借鉴。     

Bioactive secondary metabolites produced by microorganisms associated with plants

In the past few decades groups of scientists have focused their study on relatively new microorganisms called endophytes. By definition these microorganisms, mostly fungi and bacteria, colonise the intercellular spaces of the plant tissues. The mutual relationship between endophytic microorganisms and their host plants, taxanomy and ecology of endophytes are being studied. Some of these microorganisms produce bioactive secondary metabolites that may be involved in a host-endophyte relationship. Recently, many endophytic bioactive metabolites, known as well as new substances, possesing a wide variety of biological activities as antibiotic, antitumor, antiinflammatory, antioxidant, etc. have been identified. The microorganisms such as endophytes may be very interesting for biotechnological production of bioactive substances as medicinally important agents. Therefore the aim of this review is to briefly characterize endophytes and summarize the structuraly different bioactive secondary metabolites produced by endophytic microorganisms as well as microbial sources of these metabolites and their host plants.