微生物的交流信号

多年来微生物一直被认为是相对孤立的个体,在环境中独立地生存,但近些年的研究使人们认识到微生物也使用复杂多样的方式进行种内、种间,甚至与其他生物间的跨界信息交流。这些交流由特定的信号分子来完成,称之为微生物语言。借助这些交流语言使微生物在特定的生态位中与其相邻个体或种群建立了多样的互动关系,包括合作、竞争与资源共享等,通过协调群体行为,共同应对多变的环境。随着现代分子科学对自然微生物群落的不断深入研究,人们对微生物交流也逐渐有了更为清晰的认知。本综述总结了原核和真核微生物所使用的主要信号物质(如群体感应、群体猝灭、抗生素等)和交流方式,讨论了这些通讯语言在种内(同种微生物)、种间(异种微生物),以及跨界(微生物与宿主)交流上的表现。旨在更为深入地解读这一有趣的多学科交叉研究领域,更好地理解微生物交流语言的形式、机制和目的,为微生物行为的解读和生态事件的解析获取基于化学生态学的新思路。     

微生物分子生态学发展历史及研究现状

微生物群落多样性是微生物生态学和环境学研究的重点之一。分子生物学方法应用于微生物群落结构分析使得对环境样品中占大多数的不可培养微生物的研究成为了可能。由于功能上高度保守,序列上的不同位置具有不同的变异速率,核糖体RNA（rRNA）是目前在微生物分子生态学上最为有用以及应用最广泛的分子标记,通过rRNA序列比对,可以分析不同分类水平的系统发育关系。元基因组学研究方法通过对环境样品中的各种微生物群落的总的基因组进行分析,充分展示了环境微生物代谢途径,极大地扩展了对微生物的认识。快速发展的高通量测序极大地促进了各项微生物生态学技术的发展,带来了新的突破。     

Development of soil microbiology methods: from respirometry to molecular approaches

This review deals with techniques and methods used in the study of the function and development of microorganisms occurring in soil with emphasis on the contributions of Czech Academician Ivan Málek and his coworkers or fellows (Jiří Macura, František Kunc) to the development of basic techniques used in soil microbiology. Early studies, including batch cultivation and respirometric techniques, as well as later developments of percolation and continuous-flow methods of cultivation of soil microorganisms are discussed. Recent developments in the application of analytical chemistry (HPLC or GC) and of molecular biological techniques to ecological questions that have revolutionized concepts in soil microbiology and microbial ecology are also briefly mentioned, including denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), phospholipid fatty acid analysis (PLFA) and others. The shift of soil microbiology from the study of individual microorganisms to entire microbial communities, including nonculturable species, is briefly discussed.     

Application of FISH technology for microbiological analysis: current state and prospects

In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.     

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。     

水圈微生物：推动地球重要元素循环的隐形巨人

正生活在水圈环境中的微生物数量巨大、遗传与代谢方式极为多样,它们驱动着地球上重要元素的循环。水圈微生物研究已经成为生命科学与地球科学的研究热点。国家自然科学基金委员会于2017年启动了"水圈微生物驱动地球元素循环的机制"重大研究计划(简称"水圈微生物"计划)。"水圈微生物"计划拟选择典型水圈生境,通过多学科交叉研究,借助新技术、新方法,揭示水圈微生物在物种、群落和生态水平驱动碳氮硫循环的机制及其环境响应,     

Microbial diversity associated with ascidians: a review of research methods and application

This paper reviews research in microbial diversity associated with ascidians (commonly known as sea squirts). The application of culture-dependent and culture-independent techniques is introduced in detail and these methods are analyzed for their advantages and limitations. Because of the limitations of available media and cultivation conditions, culture-dependent methods can only reveal a limited portion of the microorganisms in ascidians. However, the acquisition of typical microbial community members in culture remains a valuable resource for exploring their bioactive potential and relationships with the ascidian hosts. The application of metagenomic library methods has greatly accelerated ascidian metabolites studies. The next-generation sequencing techniques have led to the acquisition of an unprecedented quantity of ascidian microorganism data, providing the most comprehensive information about ascidian microbial diversity. Ascidians provide unique ecological niches that harbor an unexpected diversity of microorganisms different from planktonic bacteria in the local seawater. Microbial communities associated with ascidians tend to be species-specific and tissue-specific. Different tissue of the same ascidian may be associated with different microbial communities.     

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, “omics” approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.     

Microbial control of plant-parasitic nematodes: a five-party interaction

Plant-parasitic nematodes cause significant economic losses to a wide variety of crops. Chemical control is a widely used option for plant-parasitic nematode management. However, chemical nematicides are now being reappraised in respect of environmental hazard, high costs, limited availability in many developing countries or their diminished effectiveness following repeated applications. This review presents progress made in the field of microbial antagonists of plant-parasitic nematodes, including nematophagous fungi, endophytic fungi, actinomycetes and bacteria. A wide variety of microorganisms are capable of repelling, inhibiting or killing plant-parasitic nematodes, but the commercialisation of these microorganisms lags far behind their resource investigation. One limiting factor is their inconsistent performance in the field. No matter how well suited a nematode antagonist is to a target nematode in a laboratory test, rational management decision can be made only by analysing the interactions naturally occurring among “host plant–nematode target–soil–microbial control agent (MCA)–environment”. As we begin to develop a better understanding of the complex interactions, microbial control of nematodes will be more fine-tuned. Multidisciplinary collaboration and integration of biological control with other control methods will␣also contribute to more successful control practices.     

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity,Growth Rate,and Cooperativeness

Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritional requirements and their ecological and genomic traits. We first show that nutritional requirements are more similar among species that co-habit many ecological niches. We then reveal three fundamental characteristics of microbial fastidiousness (i.e., complex and specific nutritional requirements): (1) more fastidious microorganisms tend to be more ecologically limited; (2) fastidiousness is positively associated with smaller genomes and smaller metabolic networks; and (3) more fastidious species grow more slowly and have less ability to cooperate with other species than more metabolically versatile organisms. These associations reflect the adaptation of fastidious microorganisms to unique niches with few cohabitating species. They also explain how non-fastidious species inhabit many ecological niches with high abundance rates. Taken together, these results advance our understanding microbial nutrition on a large scale, by presenting new nutrition-related associations that govern the distribution of microorganisms in nature.     

Structural diversity of microorganisms in chemically perturbed soil assessed by molecular and cytochemical approaches

Until recently, our understanding of microbial community development in soil ecosystems exposed to different inorganic and organic pollutants has been limited to culturable microorganisms because of the techniques available. The discovery that most soil microorganisms are non-culturable but potentially viable and metabolically active accelerated the application of different culture-independent methods for structural diversity assessments of the microbial community. This review examines the results of recent studies on the impact of heavy metals and organic pollutants on the diversity of the microflora obtained with methods based on analyses of signature biomarkers such as nucleic acids and fatty acids. The application of these techniques allowed researchers to pinpoint reduction of microbial diversity in contaminated soil, and significant shifts in the community structure, leading to the dominance of only a few populations (species) and the disappearance of others, some of which were never isolated by conventional methods (e.g. an increase in Acidobacterium or a decrease in terrestrial non-thermophilic Crenarchaeota). Although the new techniques are not free from limitations, they allow the monitoring of the virtual impact of stressors on soil microorganisms and the direction of resuscitation of the microbial community during natural or induced bioremediation, especially when using combined approaches.     

Microbial ultraviolet sunscreens

Exposure to the shortest wavelengths in sunlight, ultraviolet light, constitutes a deleterious ecological factor for many microorganisms. The use of secondary metabolites as sunscreens has emerged as an important photoprotective mechanism in certain groups of large-celled microorganisms, such as cyanobacteria, fungi and many protists. In this Review, we describe our current understanding of microbial 'sunscreen' compounds, including scytonemin, the mycosporines and the naphthalene-based melanins. Study of these sunscreens has led to the discovery of new classes of compounds, new metabolic pathways, a deeper understanding of microbial photobiology and the potential for dermatological or biomedical applications.     

Contributions of soil micro-fauna (protozoa and nematodes) to rhizosphere ecological functions

Contributions of soil micro-fauna (protozoa and nematodes) to rhizosphere ecological functions and possible modes of action were reviewed. Micro-fauna in rhizosphere play an important role in release of plant available nutrients, accumulation and stabilization of soil organic carbon, hormonal effects on roots, microbial diversity and functional stability, multi-trophic interactions above ground, and bioremediation of contaminated soils. Selective grazing, active dispersal and excretion by the micro-fauna not only benefit the rhizosphere ecological functions, but also have an impact on the whole soil and above-ground community. It appears that mechanically understanding rhizosphere ecological functions would remain incomplete without considering the interactions of micro-fauna with microorganisms and roots.     

Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.     

微生物生态学理论框架

微生物是生态系统的重要组成部分,直接或间接地参与所有的生态过程。微生物生态学是基于微生物群体的科学,利用微生物群体DNA/RNA等标志物,重点研究微生物群落构建、组成演变、多样性及其与环境的关系,在生态学理论的指导和反复模型拟合下由统计分析得出具有普遍意义的结论。其研究范围从基因尺度到全球尺度。分子生物学技术的发展,使人们可以直接从基因水平上考查其多样性,从而使得对微生物空间分布格局及其成因的深入研究成为可能。进而可以从方法学探讨微生物生物多样性、分布格局、影响机制及其对全球变化的响应等。在微生物生态学研究中,群落构建与演化、分布特征(含植物-微生物相互关系)、执行群体功能的机理(生物地球化学循环等)、对环境变化的响应与反馈机理是今后需要关注的重点领域。概述了微生物生态学的概念,并初步提出其理论框架,在对比宏观生态学基础理论和模型的基础上,分析微生物多样性的研究内容、研究方法和群落构建的理论机制,展望了今后研究的重点领域。     

根际微型土壤动物——原生动物和线虫的生态功能

从养分释放、土壤有机碳积累和稳定、根系激素效应、微生物多样性和功能稳定性、地上部多营养级关系及污染土壤生物修复概述了根际微型土壤动物(原生动物和线虫)对根际生态功能的影响,特别针对微型土壤动物与微生物和根系的相互作用探讨了可能的机制。微型土壤动物的选择取食、主动迁移和代谢分泌行为,不仅贡献根际生态功能,而且对土壤整体及地上部群落有强烈的影响。总之,不考虑根际微型土壤动物与微生物和根系的相互作用,就不可能对根际生态功能和调控机制有全面的认识。     

微生物组学的技术和方法及其应用

微生物组是指一个特定环境或生态系统中全部微生物及其遗传信息的集合, 其蕴藏着极为丰富的微生物资源。全面系统地解析微生物组的结构和功能, 将为解决人类面临的能源、生态环境、工农业生产和人体健康等重大问题带来新思路。然而, 微生物组学研究在很大程度上取决于其技术与方法的发展。在高通量测序技术出现以前, 微生物研究主要基于分离培养和指纹图谱等技术, 然而, 由于这些技术存在的缺陷, 人们对于微生物的认识十分有限。自21世纪初以来, 尽管高通量测序和质谱技术的革命性突破极大地促进了人们对于微生物的认识, 微生物组学技术在微生物组研究中的应用仍面临着诸多挑战。此外, 目前微生物组的结构和多样性等描述性研究已臻成熟, 微生物组学研究正处于从数量到质量、从结构到功能的关键转变时期。因此, 该文首先介绍了微生物组学的基本概念及其发展简史, 其次简述了微生物组学研究的相关技术和方法及其发展历程, 并进一步阐述了微生物组学的技术和方法在生态学研究中的应用及存在的主要问题, 最后从技术、理论和应用层面阐述了未来微生物组学技术和方法发展的前沿方向, 并提出了今后微生物组学研究的优先发展领域。     

Ontogenetic allometry of the bluemouth, <Emphasis Type="Italic">Helicolenus dactylopterus dactylopterus</Emphasis> (Teleostei: Scorpaenidae), in the Northeast Atlantic and Mediterranean based on geometric morphometrics

Since the emergence of the ‘microbial loop’ concept, heterotrophic flagellates have received particular attention as grazers in aquatic ecosystems. These microbes have historically been regarded incorrectly as a homogeneous group of bacterivorous protists in aquatic systems. More recently, environmental rDNA surveys of small heterotrophic flagellates in the pelagic zone of freshwater ecosystems have provided new insights. (i) The dominant phyla found by molecular studies differed significantly from those known from morphological studies with the light microscope, (ii) the retrieved phylotypes generally belong to well-established eukaryotic clades, but there is a very large diversity within these clades and (iii) a substantial part of the retrieved sequences cannot be assigned to bacterivorous but can be assigned instead to parasitic and saprophytic organisms, such as zoosporic true fungi (chytrids), fungus-like organisms (stramenopiles), or virulent alveolate parasites (Perkinsozoa and Amoebophrya sp.). All these microorganisms are able to produce small zoospores to assure dispersal in water during their life-cycles. Based on the existing literature on true fungi and fungus-like organisms, and on the more recently published eukaryotic rDNA environmental studies and morphological observations, we conclude that previously overlooked microbial diversity and related ecological potentials require intensive investigation (i) for an improved understanding of the roles of heterotrophic flagellates in pelagic ecosystems and (ii) to properly integrate the concept of ‘the microbial loop’ into modern pelagic microbial ecology.     

Dealing with water stress and microbial preservation

The relevance of preserving microorganisms has been well accepted for several decades. Interest is now shifting towards investigating adequate preservation methods to improve microbial survival rates and to preserve new taxa of previously considered unculturable microorganisms. In addition, a growing interest in preserving fragile microbial consortia or communities with biotechnological interest motivates the improvement of preservation methods. In the present study, we reviewed the effect of water availability in microbial diversity shift. We describe the effect of drought on microorganisms at the molecular level and their molecular responses to this life-threatening challenge focusing on the production of xeroprotectants. We also review the interspecies interactions of those drought-tolerant microorganisms with other sensitive organisms including neighbouring prokaryotes and eukaryotes such as plants, and the potential role of these microorganisms at determining the ecological composition of stressed environments. We emphasize the importance of applying the knowledge derived from the molecular mechanisms used by desiccation-tolerant microorganisms for the improvement of the preservation techniques. An overview of the current and newer techniques for preserving microorganisms and microbial communities is provided. The biotechnological interest in preserving pure cultures, microbial consortia and communities is also discussed.     

石生微生物研究进展

石生微生物是一类自养微生物支持下的在全球广泛分布、能较好适应极端自然条件的岩石生境微生物及微生物群落。石生生物的研究对极端环境生态适应机制、探索地外生命以及保护石质文物等方面都有重要指导作用,然而我国对石生微生物的研究罕有报道。本文从石生微生物的分类、分布、研究方法、生态适应等方面的研究进展进行综述,对石生微生物研究存在的问题进行探讨,为我国相关领域的研究提供参考。