单细胞稳定同位素标记技术在固氮微生物中的应用研究

生物固氮是指固氮微生物将大气中氮气还原为生物可利用氨的过程,是环境中新氮的主要来源,调控初级生产力并影响氮储库的收支平衡。由于环境中大部分固氮微生物不可纯培养,不依赖培养且具有高空间分辨率水平的单细胞技术,成为研究固氮微生物的有力手段。~(15)N_2稳定同位素标记技术,以微生物对~(15)N的同化量或速率为依据,是表征微生物固氮活性的最直接手段。本文对~(15)N_2稳定同位素标记结合两种单细胞技术,即纳米二次离子质谱(Nano SIMS)和单细胞拉曼光谱,用于固氮微生物研究的最新进展进行了综述,内容包括揭示环境中高活性固氮微生物、空间分布、与其他生物的共生关系、细胞生理状态等,并进一步对近期发展的基于单细胞拉曼光谱的固氮微生物研究进行了展望。     

环境异质性影响土壤微生物群落的研究进展

环境异质性是影响微生物群落结构和多样性的重要因素,其涉及内容广泛,各异质性因素之间彼此关联。基于生物和非生物特征,可将环境异质性分为土地覆盖、植物、气候、土壤和地形等5种异质性因素。文章综述了上述五种环境异质性因素的概念和区别,并针对不同类型环境异质性因素对微生物群落的影响进行了较为全面的汇总和分析。通过梳理微生物生态学、生物信息学等相关研究方法和技术的发展,阐述了现阶段研究环境异质性与微生物互作关系的不足,并进行了展望。     

海洋微生物多样性的研究进展

海洋微生物多样性（marine microorganisms diversity)是指所有海洋微生物种类、种内遗传变异和它们的生存环境的总称。本文介绍了海洋微生物多样性方面的研究和利用进展,包括研究微生物多样性方法的改进,有价值的海洋微生物功能性产品的开发;关于海洋微生物抗肿瘤、抗病毒药物的研究等。     

大洋最小含氧带生物地球化学循环及微生物多样性研究进展

大洋的最小含氧带(oxygen minimum zones,OMZs)具有特殊的水动力和氧含量特征,该区域是氮流失的主要场所,也是各类生化反应发生的重要区域.OMZs的存在会对浮游生物的丰度、多样性、分布模式及呼吸方式产生较大影响.大洋OMZs中存在广泛的反硝化、厌氧氨氧化、甲烷厌氧氧化和隐性厌氧硫氧化作用等都是海洋物...     

海洋微生物多样性及其分子生态学研究进展

海洋微生物多样性的深入研究将有助于微生物资源更好的开发和利用,海洋微生物多样性有很大的研究价值和研究空间。海洋中大多数微生物处于未可培养状态,在分子生态学基础上对海洋未可培养微生物进行研究是当今微生物多样性研究的主要方向。近年来相关研究进展迅速,研究方法不断更新。主要从分子生态学角度对微生物多样性研究现状进行概述并详细分析探讨了相关的研究方法,而且从分子生态学与海洋微生物多样性研究相结合的层面,对本领域的研究进行展望。旨在为海洋微生物多样性的研究及海洋资源的可持续开发与利用提供参考。     

驯化对生物阴极微生物燃料电池中阴极微生物群落多样性的影响

【背景】生物阴极微生物燃料电池因其构造成本低和阴极可持续性发展的优点而成为一种很有前途的废水处理系统,但阴极微生物的氧化还原性能限制了其在实际应用中的推广。【目的】为了提高生物阴极的性能,需要深入了解影响阴极氧化还原性能的微生物群落。【方法】利用16S rRNA基因高通量测序技术分析对比原始接种污泥样品和驯化后阴极电极上生物膜样品多样性及结构变化。【结果】测序结果表明,原始接种污泥样品与驯化后阴极电极生物膜样品中微生物群落种类和结构存在显著差异,驯化后阴极电极生物膜样品中变形菌门(Proteobacteria)、γ-变形菌纲(Gammaproteobacteria)和特吕珀菌属(Trueperaceae)相对丰度比例高于原始污泥样品,成为优势菌群。【结论】驯化对系统阴极电极生物膜群落影响显著,随着产电量的输出,优势菌群不断富集,最终形成一个适应该实验环境下的新的微生物群落。对优势菌群结构和变化进行探讨,为生物阴极的研究补充更多生物学方面的理论基础。     

海洋微生物多样性研究技术进展

海洋微生物资源丰富,开发潜力巨大,综述了稀释培养、高通量培养、扩散盒培养和微囊包埋等新的海洋微生物可培养技术的发展,重点阐述了基于现代分子技术的PCR、DGGE/TGGE、gyrB基因、基因芯片、环境基因组学和质谱等方法在未培养海洋微生物多样性研究中的应用。通过上述研究技术和方法的创新,人类开发海洋微生物资源进入一个崭新的时代。     

冰川生态系统固碳微生物研究进展

[目的] 海南海口含有丰富的温泉资源,对温泉微生物多样性进行研究,有助于进一步开发和利用海南温泉微生物资源。[方法] 本文采用Illumina HiSeq高通量测序技术对海口3个温泉[海甸岛荣域温泉（S1）、火山口开心农场温泉（S2）和西海岸海长流温泉（S3）] 水样中微生物ITS序列和16S rRNA基因V3-V4区进行测序及生物信息学分析,探究海口市3个不同区域的温泉真菌多样性与细菌多样性。[结果] （1）α多样性分析表明,真菌群落中,S3 > S1 > S2,而在细菌群落中,S2 > S1 > S3。β多样性分析表明,3个温泉真菌群落和细菌群落组成差异皆显著。（2）分类分析表明,温泉真菌群落优势菌门为子囊菌门（Ascomycota）和担子菌门（Basidiomycota）,细菌群落优势菌门为变形菌门（Proteobacteria）、拟杆菌门（Bacteroidetes）、Thermi、硝化螺旋菌门（Nitrospirae）、绿菌门（Chlorobi）、厚壁菌门（Firmicutes）、绿弯菌门（Chloroflexi）、放线菌门（Actinobacteria）。（3）CCA（Canonical correspondence analysis）分析表明,3个温泉的真菌群落主要影响因子是温度,细菌群落主要影响因子是总磷。[结论] 海南省海口市温泉中含有丰富的微生物资源,其微生物群落组成受多种环境因子影响,且影响真菌和细菌的主要环境因子不同。     

基于Illumina MiSeq高通量测序技术分析硇洲岛海星共附生微生物多样性

【背景】海星作为海洋生物中的一类比较高级的棘皮类动物,其体内蕴藏着丰富且具有生物活性的共附生微生物资源。【目的】分析湛江硇洲岛海星中共附生微生物的多样性。【方法】采用IlluminaMiSeq高通量测序技术分别对硇洲岛海星进行共附生细菌16SrRNA基因V3-V4区和共附生真菌18S rRNA基因ITS1-ITS2区的测序,并根据测序结果进行OTU聚类分析、α多样性分析及物种分类分析等。【结果】高通量测序获得细菌和真菌Filtered的数目分别为61992和71196个,OTU数目分别为2384和529个。经物种分类分析,共附生细菌主要为变形菌门(Proteobacteria),其平均相对含量高达77.37%;其次是厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteria)和梭杆菌门(Fusobacteria);其中优势细菌属为嗜冷杆菌属(Psychrobacter)和乳球菌属(Lactococcus)。共附生真菌主要为子囊菌门(Ascomycota),其相对含量高达92.33%;其次是霉菌门(Fungi)、担子菌门(Basidi...     

454测序技术在微生物生态学研究中的应用

以Sanger法(双脱氧核苷酸末端终止法)为代表的第1代测序技术由于其成本高、速度慢、通量低等不足,满足不了大规模测序的要求.进入21世纪后,以Roche 454为代表的第2代测序技术诞生了,454测序法作为一种高通量的测序方法,近年来已被广泛应用于微生物生态学研究中.介绍了该测序技术的原理和操作步骤,结合本实验室的研...     

Microbes: the hidden giant behind the biogeochemical cycling of elements in the hydrosphere

<正>Microbes are the oldest inhabitants of Earth. Through billions of years of coevolution with Earth, these creatures,usually invisible to the naked eye, have contributed to shaping the Earth surface, creating an ecosystem habitable for higher organisms including humans. By some estimates,microbes account for up to half of the biomass on the planet today (Whitman et al., 1998). They thrive in every corner of Earth, including harsh habitats such as hot springs, hydro-     

Expanding the Entamoeba Universe: New Hosts Yield Novel Ribosomal Lineages

Removing the requirement for cell culture has led to a substantial increase in the number of lineages of Entamoeba recognized as distinct. Surveying the range of potential host species for this parasite genus has barely been started and it is clear that additional sampling of the same host in different locations often identifies additional diversity. In this study, using small subunit ribosomal RNA gene sequencing, we identify four new lineages of Entamoeba, including the first report of Entamoeba from an elephant, and extend the host range of some previously described lineages. In addition, examination of microbiome data from a number of host animals suggests that substantial Entamoeba diversity remains to be uncovered.     

Microbial diversity: the importance of exploration and conservation

Microbial diversity is fundamental to maintenance and conservation of global genetic resources. As extreme environments are explored, the richness of microbial diversity is increasingly evident. Measures must be taken to estimate, record, and conserve microbial diversity, not only to sustain human health but also to enrich the human condition globally through wise use and conservation of genetic resources of the microbial world. Received 24 April 1996/ Accepted in revised form 07 January 1997     

Patterns and governing forces in aquatic microbial communities

In this review we survey recent publications employing molecular techniques to investigate the distribution of microbial species in aquatic environments. We analyzed the occurrence of microbial phyla in freshwater and marine habitats and observed patterns of distribution that could be explained by the adaptation of microorganisms to physical and biological parameters that vary in aquatic habitats. The gram-positive bacteria, the Verrucomicrobiales and the - and -subdivisions of the Proteobacteria are distributed throughout a range of aquatic habitats, while other phylogenetic groups appear to be adapted to more narrowly defined environmental niches such as anoxic water and sediments (-Proteobacteria) or floating aggregates (Cytophaga-Flexibacter-Bacteroides phylum). -proteobacterial sequence types have been detected throughout freshwater habitats, but these organisms are largely absent from open ocean environments. Within several of these divisions, clusters of closely related small sub unit ribosomal RNA sequence types have been detected in geographically disparate environments, suggesting that some microbial species are globally distributed. In addition to physical variables such as salinity and pH, biological variables also influence microbial community composition. This was illustrated by changes that occurred in the eukaryotic and bacterial species composition in laboratory mesocosms after a viral outburst. We conclude that physical and biological forces govern the composition of aquatic microbial communities and result in divergent evolutionary histories of the indigenous microbial species.     

Localization of mitochondrial ribosomal RNA on the chromatoid bodies of marine planarian polyclad embryos

Electron-dense cytoplasmic structures, referred to as chromatoid bodies, are observed in the somatic stem cells, called neoblasts, and germline cells in adult planarians. Although it has been revealed that the chromatoid bodies morphologically resemble germline granules in Drosophila and Xenopus embryos, what essential role it plays in the planarian has remained unclear. In the present study, to examine whether chromatoid bodies in planarian embryos are responsible for germline formation, the presence and behavior of chromatoid bodies during embryogenesis were examined. Mitochondrial large ribosomal RNA and mitochondrial small ribosomal RNA were used as candidate markers for components of the chromatoid body. Starting from the fertilized egg, extramitochondrial signals of both RNA (mtrRNA) were observed. At the ultrastructural level, mtrRNA were localized on the surface of the chromatoid bodies. At subsequent stages, the signals of mtrRNA were observed in certain restricted blastomeres that contribute to the formation of larval structures. The signals gradually decreased from the gastrula stage. These results suggest that the chromatoid bodies associated with mtrRNA in embryogenesis are not germline granules. The chromatoid bodies of blastomeres may be concerned with the toti- or pluripotency and cell differentiation as proposed in adult planarian neoblasts.     

微生物学课程中的微生物多样性教学内容的改革

为了强调物种多样性在微生物学课程中的分量,近几年我们尝试对教学内容进行了改革：①将微生物分类单元、细胞生物的拉丁双名法等共性分类知识调到绪论中;②在讲授原核微生物、真核微生物和病毒各章时,分别增加了它们的多样性与分类内容;③考虑到课时所限,采用图表概括方式介绍各大类微生物的主要分类类群及主要特征,将原先课堂教学中介绍的一些特殊微生物内容纳入到微生物多样性体系中讲解,适当予以详细介绍,     

Microbial diversity in the tick Argas japonicus (Acari: Argasidae) with a focus on Rickettsia pathogens

The soft tick Argas japonicus mainly infests birds and can cause human dermatitis; however, no pathogen has been identified from this tick species in China. In the present study, the microbiota in A. japonicus collected from an epidemic community was explored, and some putative Rickettsia pathogens were further characterized. The results obtained indicated that bacteria in A. japonicus were mainly ascribed to the phyla Proteobacteria, Firmicutes and Actinobacteria. At the genus level, the male A. japonicus harboured more diverse bacteria than the females and nymphs. The bacteria Alcaligenes, Pseudomonas, Rickettsia and Staphylococcus were common in nymphs and adults. The abundance of bacteria belonging to the Rickettsia genus in females and males was 7.27% and 10.42%, respectively. Furthermore, the 16S rRNA gene of Rickettsia was amplified and sequenced, and phylogenetic analysis revealed that 13 sequences were clustered with the spotted fever group rickettsiae (Rickettsia heilongjiangensis and Rickettsia japonica) and three were clustered with Rickettsia limoniae, which suggested that the characterized Rickettsia in A. japonicus were novel putative pathogens and also that the residents were at considerable risk for infection by tick‐borne pathogens.     

树种多样性对土壤微生物群落结构和元素生物地球化学循环的影响研究进展

森林是陆地生态系统的重要组成部分,其巨大的生产力和生态服务功能对人类的生存和发展至关重要。森林树种多样性增加能够显著提高森林生产力,关于树种多样性如何影响地下生物多样性及生态功能逐渐受到国内外学者的广泛关注。从土壤微生物及其介导的元素生物地球化学循环这一视角出发,综述了树种多样性对土壤细菌和真菌多样性、群落结构及功能的影响,提出需要进一步深入研究的方向。总体来说,树种多样性有利于增加土壤细菌生物量和多样性,是预测病原性真菌和菌根真菌多样性及群落结构的重要生物因子。树种多样性能增加土壤有机碳储量,增强森林土壤的甲烷氧化能力,并提高土壤磷周转速率及有效磷含量。关于树种多样性对森林土壤氮循环的影响需考虑多样性假说和质量比假说的相对贡献。今后应加强树种多样性对多个营养级之间相互作用的研究;关注树种多样性对生态系统多功能的影响;加强学科交叉,引入微生物种群动态模型和气候模型等模型预测方法,研究树种多样性对全球气候变化的应对机制,以期促进地上植物多样性与地下生态系统功能关系的研究,增强森林生态系统应对未来全球环境变化的能力。