The Earth's bounty: assessing and accessing soil microbial diversity.

The study of microbial diversity represents a major opportunity for advances in biology and biotechnology. Recent progress in molecular microbial ecology shows that the extent of microbial diversity in nature is far greater than previously thought. Here, we discuss methods to analyse microorganisms from natural environments without culturing them and new approaches for gaining access to the genetic and chemical resources of these microorganisms.     

Life under Nutrient Limitation in Oligotrophic Marine Environments: An Eco/Physiological Perspective of <Emphasis Type="Italic">Sphingopyxis alaskensis</Emphasis> (formerly <Emphasis Type="Italic">Sphingomonas alaskensis</Emphasis>)

The oceans of the world are nutrient-limited environments that support a dynamic diversity of microbial life. Heterotrophic prokaryotes proliferate in oligotrophic regions and affect nutrient transformation and remineralization thereby impacting directly on the all marine biota. An important challenge in studying the microbial ecology of oligotrophic environments has been the isolation of ecologically important species. This goal has been recognized not only for its relevance in defining the dynamics of community composition, but for enabling physiological studies of competitive species and inferring their impact on the microbial food web. This review describes the successful isolation attempts of the ultramicrobacterium, Sphingopyxis alaskensis (formerly described as Sphingomonas alaskensis) using extinction dilution culturing methods. It then provides a comprehensive perspective of the unique physiological and genetic properties that have been identified that distinguish it from typical copiotrophic species. These properties are described through studies of the growth phase and growth rate control of macromolecular synthesis, stress resistance and global gene expression (proteomics). We also discuss the importance of integrating ecological and physiological approaches for studying microorganisms in marine environments.     

Developments in aquatic microbiology.

Major discoveries in marine microbiology over the past 4-5 decades have resulted in the recognition of bacteria as a major biomass component of marine food webs. Such discoveries include chemosynthetic activities in deep-ocean ecosystems, survival processes in oligotrophic waters, and the role of microorganisms in food webs coupled with symbiotic relationships and energy flow. Many discoveries can be attributed to innovative methodologies, including radioisotopes, immunofluorescent-epifluorescent analysis, and flow cytometry. The latter has shown the key role of marine viruses in marine system energetics. Studies of the components of the "microbial loop" have shown the significance of various phagotrophic processes involved in grazing by microinvertebrates. Microbial activities and dissolved organic carbon are closely coupled with the dynamics of fluctuating water masses. New biotechnological approaches and the use of molecular biology techniques still provide new and relevant information on the role of microorganisms in oceanic and estuarine environments. International interdisciplinary studies have explored ecological aspects of marine microorganisms and their significance in biocomplexity. Studies on the origins of both life and ecosystems now focus on microbiological processes in the marine environment. This paper describes earlier and recent discoveries in marine (aquatic) microbiology and the trends for future work, emphasizing improvements in methodology as major catalysts for the progress of this broadly-based field.     

Exploring mixed microbial community functioning: recent advances in metaproteomics

System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.     

Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities

A major research goal in microbial ecology is to understand the relationship between gene organization and function involved in environmental processes of potential interest. Given that more than an estimated 99% of microorganisms in most environments are not amenable to culturing, methods for culture-independent studies of genes of interest have been developed. The wealth of metagenomic approaches allows environmental microbiologists to directly explore the enormous genetic diversity of microbial communities. However, it is extremely difficult to obtain the appropriate sequencing depth of any particular gene that can entirely represent the complexity of microbial metagenomes and be able to draw meaningful conclusions about these communities. This review presents a summary of the metagenomic approaches that have been useful for collecting more information about specific genes. Specific subsets of metagenomes that focus on sequence analysis were selected in each metagenomic studies. This 'targeted metagenomics' approach will provide extensive insight into the functional, ecological and evolutionary patterns of important genes found in microorganisms from various ecosystems.     

Marine sponges and their microbial symbionts: love and other relationships

Many marine sponges harbour dense and diverse microbial communities of considerable ecological and biotechnological importance. While the past decade has seen tremendous advances in our understanding of the phylogenetic diversity of sponge-associated microorganisms (more than 25 bacterial phyla have now been reported from sponges), it is only in the past 3-4 years that the in situ activity and function of these microbes has become a major research focus. Already the rewards of this new emphasis are evident, with genomics and experimental approaches yielding novel insights into symbiont function. Key steps in the nitrogen cycle [denitrification, anaerobic ammonium oxidation (Anammox)] have recently been demonstrated in sponges for the first time, with diverse bacteria - including the sponge-associated candidate phylum 'Poribacteria'- being implicated in these processes. In this minireview we examine recent major developments in the microbiology of sponges, and identify several research areas (e.g. biology of viruses in sponges, effects of environmental stress) that we believe are deserving of increased attention.     

海洋动物来源微生物分离培养的新方法

海洋动物体内有着丰富的微生物,它们可以帮助动物宿主合成一些营养物质或者抵御其他动物侵害所需的化合物。在海洋动物来源微生物的生物活性化合物中,目前已有功能较好且应用于临床治疗的化合物。由于实验室分离培养条件的限制,目前仅有小部分的微生物被分离利用。因此开展新颖而有效的海洋动物来源微生物分离培养方法的研究十分必要。本文概括了近些年从海洋动物中分离微生物的新方法的结果和不足,这些方法包括原位培养技术、电回收法和培养基的改良等,重点介绍了扩散盒技术、I-tip技术和微囊包埋技术等。这些新方法的应用有助于获得更多新的微生物菌种和微生物次生代谢产物,了解微生物与动物宿主之间的关系,以及扩大海洋微生物资源的开发和利用。     

Oligosaccharide recognition signals and defence reactions in marine plant-microbe interactions.

Recent findings on the involvement of oligosaccharide signals in pathogen recognition and defence reactions in marine algae shine a new light on the ecology of their interactions with associated microorganisms. Since the marine environment encompasses lineages that have diverged a long time ago from the terrestrial phyla, these results suggest that cell-cell recognition pathways typical of terrestrial plants appeared very early in the evolution of eukaryotes. Production of oligosaccharides from marine algae using microbial recombinant polysaccharidases is also of industrial interest as plants can be protected from infections by preincubation in the presence of appropriate signals that mimic the attacks by pathogens.     

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。     

Searching for microbial contribution to micritization of shallow marine sediments

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ ‘fishing’ strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.     

Phylogenetic approaches for studying diversification

Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever‐accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non‐equilibrium theories recognising the crucial role of history.     

In-depth analyses of marine microbial community genomics

Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using community genomics, DeLong et al. highlight deduced biological differences that result from open-ocean depth gradients. The power of the large-insert libraries used is that both phylogeny and function can be inferred from the genetic material obtained--even for uncultured microbes. Together with complete genomes of marine isolates and advances in physiology and ecology, this study paves the way for ecosystems biology approaches to dynamics and controls of marine microbial populations.     

分子生物学方法在环境微生物生态学中的应用研究进展

随着分子生物学方法的不断发展和改进,微生物在生态系统中的作用被更好的挖掘出来。目前快速发展的先进的分子生物学技术,已经开始应用于分析环境微生物的多样性、微生物的生物地理学及微生物对气候变化的响应等。一般环境微生物的研究目标主要有3个,即确定微生物的种类和多样性、微生物的功能或潜在作用及在特定时间点活跃的微生物等。然而,现有微生物的研究方法复杂多样,容易给研究者在方法的选择上带来困惑。将从微生物的多样性和功能研究两个方面介绍和分析相应的分子生物学方法,尤其是近年来快速发展的高通量测序、宏组学和单细胞水平研究方法(如纳米二次离子质谱与荧光原位杂交相结合的方法)等新技术及其应用情况,以期为研究者选择合适的研究方法进行环境微生物的研究提供依据。     

Environmental diversity of bacteria and archaea

The microbial way of life spans at least 3.8 billion years of evolution. Microbial organisms are pervasive, ubiquitous, and essential components of all ecosystems. The geochemical composition of Earth's biosphere has been molded largely by microbial activities. Yet, despite the predominance of microbes during the course of life's history, general principles and theory of microbial evolution and ecology are not well developed. Until recently, investigators had no idea how accurately cultivated microorganisms represented overall microbial diversity. The development of molecular phylogenetics has recently enabled characterization of naturally occurring microbial biota without cultivation. Free from the biases of culture-based studies, molecular phylogenetic surveys have revealed a vast array of new microbial groups. Many of these new microbes are widespread and abundant among contemporary microbiota and fall within novel divisions that branch deep within the tree of life. The breadth and extent of extant microbial diversity has become much clearer. A remaining challenge for microbial biologists is to better characterize the biological properties of these newly described microbial taxa. This more comprehensive picture will provide much better perspective on the natural history, ecology, and evolution of extant microbial life.     

组学技术在产油微生物中的应用

微生物油脂是未来燃料和食品用油的重要潜在资源。近年来,随着系统生物学技术的快速发展,从全局角度理解产油微生物生理代谢及脂质积累的特征成为研究热点。组学技术作为系统生物学研究的重要工具被广泛用于揭示产油微生物脂质高效生产的机制研究中,这为产油微生物理性遗传改造和发酵过程控制提供了基础。文中对组学技术在产油微生物中的应用概况进行了综述,介绍了产油微生物组学分析常用的样品前处理及数据分析方法,综述了包括基因组、转录组、蛋白(修饰)组及代谢(脂质)组等在内的多种组学技术,以及组学数据基础上的数学模型在揭示产油微生物脂质高效生产机制中的研究,并对未来发展和应用进行了展望。     

Biotechnological production of eicosapentaenoic acid: From a metabolic engineering point of view

Eicosapentaenoic acid (EPA) is an ω3 polyunsaturated fatty acid which has been demonstrated to play important roles in a number of aspects of human health. EPA is traditionally obtained from marine fish oils. However, the shrinking fish populations are making the sustainability of these sources questionable. Consequently, alternative sources of EPA are being sought, especially from marine microalgae, bacteria, and fungi. These microorganisms contain relatively large amounts of high-quality EPA and they are the primary producers of this important fatty acid. There are two distinct pathways for EPA de novo biosynthesis in microbial systems: the desaturation and elongation pathway and the polyketide pathway. Genes involved in the biosynthetic pathways have been identified from different microorganisms and characterized in depth. In addition, numerous strategies have been developed for commercial production of EPA by microbial fermentation, among which strain improvements by genetic engineering could provide high-yield producers of EPA. In this review, we summarize recent efforts and experiences devoted to metabolic engineering of various microorganisms that lead to efficient biocatalysts for the production of EPA, as well as the key limitations and challenges. The combination of traditional biochemistry and molecular biology with new systems biology and synthetic biology tools will provide a better view of EPA biosynthesis and a greater potential of microbial production. Continued advances in metabolic engineering will help to improve the final titer, productivity, and yield of EPA.     

Symbiont genomics,our new tangled bank

Microbial symbionts inhabit the soma and surfaces of most multicellular species and instigate both beneficial and harmful infections. Despite their ubiquity, we are only beginning to resolve major patterns of symbiont ecology and evolution. Here, we summarize the history, current progress, and projected future of the study of microbial symbiont evolution throughout the tree of life. We focus on the recent surge of data that whole-genome sequencing has introduced into the field, in particular the links that are now being made between symbiotic lifestyle and molecular evolution. Post-genomic and systems biology approaches are also emerging as powerful techniques to investigate host–microbe interactions, both at the molecular level of the species interface and at the global scale. In parallel, next-generation sequencing technologies are allowing new questions to be addressed by providing access to population genomic data, as well as the much larger genomes of microbial eukaryotic symbionts and hosts. Throughout we describe the questions that these techniques are tackling and we conclude by listing a series of unanswered questions in microbial symbiosis that can potentially be addressed with the new technologies.     

环境DNA技术在地下生态学中的应用

地下生态过程是生态系统结构、功能和过程研究中最不确定的因素。由于技术和方法的限制,作为"黑箱"的地下生态系统已经成为限制生态学发展的瓶颈,也是未来生态学发展的主要方向。环境DNA技术,是指从土壤等环境样品中直接提取DNA片段,然后通过DNA测序技术来定性或定量化目标生物,以确定目标生物在生态系统中的分布及功能特征。环境DNA技术已成功用于地下生态过程的研究。目前,环境DNA技术在土壤微生物多样性及其功能方面的研究相对成熟,克服了土壤微生物研究中不能培养的问题,可以有效地分析土壤微生物的群落组成、多样性及空间分布,尤其是宏基因组学技术的发展,使得微生物生态功能方面的研究成为可能;而且,环境DNA技术已经在土壤动物生态学的研究中得到了初步应用,可快速分析土壤动物的多样性及其分布特征,更有效地鉴定出未知的或稀少的物种,鉴定土壤动物类群的幅度较宽;部分研究者通过提取分析土壤中DNA片段信息对生态系统植物多样性及植物分类进行了研究,其结果比传统的植物分类及物种多样性测定更精确,改变了以往对植物群落物种多样性模式的理解。同时,环境DNA技术克服传统根系研究方法中需要洗根、分根、只能测定单物种根系的局限,降低根系研究中细根区分的误差,并探索性地用于细根生物量的研究。主要综述了基于环境DNA技术的分子生物学方法在土壤微生物多样性及功能、土壤动物多样性、地下植物多样性及根系生态等地下生态过程研究中的应用进展。环境DNA技术对于以土壤微生物、土壤动物及地下植物根系为主体的地下生态学过程的研究具有革命性意义,并展现出良好的应用前景。可以预期,分子生物学技术与传统的生态学研究相结合将成为未来地下生态学研究的一个发展趋势。     

微生物分子生态学技术在污水处理系统中的应用

微生物分子生态学作为分子生物学与微生物生态学交叉而形成的学科,在污水处理方面广泛应用。本文从分子生态学实验技术角度,综述了目前污水处理系统中微生物群体结构、多样性及其与功能相关性的研究进展,探讨了分子生态学技术的发展与应用前景,并指出研究该体系微生物对于认识微生物系统发育地位具有重要意义。