Limited versus unlimited membership in microbial communities: evaluation and experimental tests of some paradigms

Recent developments in community ecology have allowed for the synthesis of community models based on principles of limited and unlimited membership. In this discussion, these developments are used as a framework for evaluating the validity of three paradigms that have constrained research on aquatic microbial communities. Because microbes are considered to possess global distributions, species availability is not generally considered to be an important factor determining microbial community composition in most habitats. Requirements for the global distribution of a species are not the same as those for unlimited availability. Rates of propagule transport to isolated and newly formed aquatic systems ( 4 years old) are low enough to have a strong effect on microbial community composition. Natural aquatic systems may require several years to accumulate a full complement of species adapted to environmental conditions at a particular time. Except under extreme circumstances, environmental conditions are not considered to constrain membership in aquatic microbial communities. Most evidence for this contention is based on an inability to detect simple relationships between species distributions and levels of individual environmental parameters. Environmental measurements are often made at a spatial scale much greater than that of the local environment of microbes. Biotic interactions, such as competition, are generally considered to be the predominant force structuring aquatic microbial communities. Although there is an extensive laboratory database to suggest the importance of different types of species interactions, there have been few field studies to confirm this. A general research protocol is described to test predictions derived from current theory of microbial community organization. A mesocosm approach is advocated in order to incorporate crucial aspects of environmental realism into experimental designs while maintaining some of the control found in the laboratory.     

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing

The gastrointestinal tract contains a vast community of microbes that to this day remain largely unculturable, making studies in this area challenging. With the newly affordable advanced sequencing technology, important breakthroughs in this exciting field are now possible. However, standardized methods of sample collection, handling, and DNA extraction have yet to be determined. To help address this, we investigated the use of 5 common DNA extraction methods on fecal samples from 5 different species. Our data show that the method of DNA extraction impacts DNA concentration and purity, successful NGS amplification, and influences microbial communities seen in NGS output dependent on the species of fecal sample and the DNA extraction method used. These data highlight the importance of careful consideration of DNA extraction method used when designing and interpreting data from cross species studies.     

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

Metagenomic sequencing has contributed important new knowledge about the microbes that live in a symbiotic relationship with humans. With modern sequencing technology it is possible to generate large numbers of sequencing reads from a metagenome but analysis of the data is challenging. Here we present the bioinformatics pipeline MEDUSA that facilitates analysis of metagenomic reads at the gene and taxonomic level. We also constructed a global human gut microbial gene catalogue by combining data from 4 studies spanning 3 continents. Using MEDUSA we mapped 782 gut metagenomes to the global gene catalogue and a catalogue of sequenced microbial species. Hereby we find that all studies share about half a million genes and that on average 300 000 genes are shared by half the studied subjects. The gene richness is higher in the European studies compared to Chinese and American and this is also reflected in the species richness. Even though it is possible to identify common species and a core set of genes, we find that there are large variations in abundance of species and genes.     

All together now: experimental multispecies biofilm model systems

Studies of microorganisms have traditionally focused on single species populations, which have greatly facilitated our understanding of the genetics and physiology that underpin microbial growth, adaptation and biofilm development. However, given that most microorganisms exist as multispecies consortia, the field is increasingly exploring microbial communities using a range of technologies traditionally limited to populations, including meta‐omics based approaches and high resolution imaging. The experimental communities currently being explored range from relatively low diversity, for example, two to four species, to significantly more complex systems, comprised of several hundred species. Results from both defined and undefined communities have revealed a number of emergent properties, including improved stress tolerance, increased biomass production, community level signalling and metabolic cooperation. Based on results published to date, we submit that community‐based studies are timely and increasingly reveal new properties associated with multispecies consortia that could not be predicted by studies of the individual component species. Here, we review a range of defined and undefined experimental systems used to study microbial community interactions.     

Post-mortem volatiles of vertebrate tissue

Volatile emission during vertebrate decay is a complex process that is understood incompletely. It depends on many factors. The main factor is the metabolism of the microbial species present inside and on the vertebrate. In this review, we combine the results from studies on volatile organic compounds (VOCs) detected during this decay process and those on the biochemical formation of VOCs in order to improve our understanding of the decay process. Micro-organisms are the main producers of VOCs, which are by- or end-products of microbial metabolism. Many microbes are already present inside and on a vertebrate, and these can initiate microbial decay. In addition, micro-organisms from the environment colonize the cadaver. The composition of microbial communities is complex, and communities of different species interact with each other in succession. In comparison to the complexity of the decay process, the resulting volatile pattern does show some consistency. Therefore, the possibility of an existence of a time-dependent core volatile pattern, which could be used for applications in areas such as forensics or food science, is discussed. Possible microbial interactions that might alter the process of decay are highlighted.     

Testing the functional significance of microbial composition in natural communities

Ecologists have long studied the relationship between biotic composition and ecosystem functioning in larger organisms; however, only recently has this relationship been investigated widely in microorganisms. Recent studies are reviewed within a framework of three experimental approaches that are often used to study larger organisms: environmental treatment, common garden, and reciprocal transplant experiments. Although the composition of microorganisms cannot be easily manipulated in the field, applying these approaches to intact microbial communities can begin to tease apart the effects of microbial composition from environmental parameters on ecosystem functioning. The challenges in applying these approaches to microorganisms are highlighted and it is discussed how the experimental approach and duration affects a study's interpretation. In general, long-term environmental treatment experiments identify correlative relationships between microbial composition and ecosystem functioning, whereas short-term common garden experiments demonstrate that microbial composition influences ecosystem functioning. Finally, reciprocal transplants simultaneously test for interactive effects of the environment and composition on functioning. The studies reviewed provide evidence that, at least in some cases, microbial composition influences ecosystem functioning. It is concluded that whole-community experiments offer a way to test whether information about microbial composition will help predict ecosystem responses to global change.     

土壤动物肠道微生物多样性研究进展

随着分子生物学技术方法的快速发展,动物肠道微生物已成为医学、动物生理学与微生物生态学等研究领域热点。土壤动物种类繁多,分布广泛,其作为陆地生态系统重要组分,是驱动生态系统功能的关键因子。土壤动物体内的微生物由于与宿主长期共存,在与宿主协同进化中形成了丰富多样的群落结构,能够影响土壤动物本身的健康,进而介导土壤动物生态功能的实现。近些年,土壤动物肠道微生物工作方兴未艾,日渐得到重视。总结了四个部分内容：1)首先总结了土壤动物肠道微生物多样性领域的研究现状,该领域年发文量逐年增长,且近十年增长快速。土壤模式生物肠道微生物多样性研究较多且更为深入。土壤动物肠道微生物多样性组成与驱动机制、共存机制及群落构建的理论研究是该领域前沿;2)进而展示了土壤动物肠道微生物多样性组成和研究方法,土壤动物肠道菌群组成以变形菌门、厚壁菌门、放线菌门和拟杆菌门为主。早期工作基于传统分离培养,近年来新一代测序技术推动了该领域发展;3)接着关注了土壤动物肠道微生物的生态学功能,总体上体现在肠道微生物能帮助宿主分解食物基质、参与营养利用、影响寿命和繁殖及提高宿主免疫能力,且其能够影响土壤动物的气体排放及介导其对生态系...     

Life on Mars

Abstract

There is evidence that at one time Mars had liquid water habitats on its surface. Studies of microbial communities in cold and dry environments on the Earth provide a basis for discussion of the possible nature of any life that may have existed on Mars during that time. Of particular relevance are the cyanobacterial communities found in hypolithic and endolithic habitats in deserts. Microbial mats found under ice-covered lakes provide an additional possible Martian system. Results obtained from these field studies can be used to guide the search for fossil evidence of life on Mars. It is possible that in the future life will be reintroduced on Mars in an effort to restore that planet to habitable conditions. In this case the organisms under study as exemplars of past life may provide the hardy stock of pioneering Martian organisms. These first organisms must be followed by plants. The feasibility of reviving Mars will depend on the ability of plants to grow in an abundance of CO₂ but at extremely low pressures, temperatures, O₂, and N₂ levels. On Mars, biology was, and is, destiny.     

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。     

热带森林的低密度种及其形成与维持机制

低密度种指在热带森林中存在的成年个体密度很低的物种,是热带森林中树种的主要存在形式。对低密度种的认识和保护是热带森林生物多样性保育的关键之一。与稀有种相比,低密度种的含义更为广阔,它还包括那些密度低、分布范围广和绝对个体数量大的物种。低密度种形成的主要原因是母树附近的幼苗和种子的存活率较低,密度制约和有限更新也是低密度种形成的重要原因。维持低密度种最重要的外部原因是昆虫较强的飞行能力和传粉能力,而其最重要的内部原因是低密度种的生殖特性。     

Microbial toxins in plant-pathogen interactions: Biosynthesis,resistance mechanisms,and significance

In the history of phytopathology, microbial toxins have been the objects of extensive studies as possible pathogenicity or virulence factors for the producer pathogens. The recent development of molecular genetic techniques provided an experimental basis to thoroughly test the role of these secondary metabolites in pathogenesis. Some of them did prove to be highly associated with disease initiation or enhanced virulence in certain plant-pathogen interactions. In this review, we describe recent progresses in the field of plant-pathogen interactions focusing on two toxins; i.e., tabtoxin from Pseudomonas syringae and trichothecenes from Fusarium and other fungi. These microbial toxins have convincingly been shown to play causal roles in plant disease development. Studies on the biosynthesis and resistance mechanisms of these producers are outlined, and the significance of this knowledge is discussed in relation to practical applications in agriculture.     

Unraveling the resistance of microbial biofilms: has proteomics been helpful?

Biofilms are surface-attached, matrix-encased, structured microbial communities which display phenotypic features that are dramatically different from those of their free-floating, or planktonic, counterparts. Biofilms seem to be the preferred mode of growth of microorganisms in nature, and at least 65% of all human infections are associated with biofilms. The most notable and clinically relevant property of biofilms is their greater resistance to antimicrobials compared with their planktonic counterparts. Although both bacterial and fungal biofilms display this phenotypic feature, the exact mechanisms underlying their increased drug resistance are yet to be determined. Advances in proteomics techniques during the past decade have facilitated in-depth analysis of the possible mechanisms underpinning increased drug resistance in biofilms. These studies have demonstrated the ability of proteomics techniques to unravel new targets for combating microbial biofilms. In this review, we discuss the putative drug resistance mechanisms of microbial biofilms that have been uncovered by proteomics and critically evaluate the possible contribution of the new knowledge to future development in the field. We also summarize strategic uses of novel proteomics technologies in studies related to drug resistance mechanisms of microbial biofilms.     

The fructan syndrome: Evolutionary aspects and common themes among plants and microbes

Fructans are multifunctional fructose‐based water soluble carbohydrates found in all biological kingdoms but not in animals. Most research has focused on plant and microbial fructans and has received a growing interest because of their practical applications. Nevertheless, the origin of fructan production, the so‐called “fructan syndrome,” is still unknown. Why fructans only occur in a limited number of plant and microbial species remains unclear. In this review, we provide an overview of plant and microbial fructan research with a focus on fructans as an adaptation to the environment and their role in (a)biotic stress tolerance. The taxonomical and biogeographical distribution of fructans in both kingdoms is discussed and linked (where possible) to environmental factors. Overall, the fructan syndrome may be related to water scarcity and differences in physicochemical properties, for instance, water retaining characteristics, at least partially explain why different fructan types with different branching levels are found in different species. Although a close correlation between environmental stresses and fructan production is quite clear in plants, this link seems to be missing in microbes. We hypothesize that this can be at least partially explained by differential evolutionary timeframes for plants and microbes, combined with potential redundancy effects.     

The diversity of microbes: resurgence of the phenotype

The introduction of molecular genetic methods has caused confusion about the nature of microbial species. Environmental DNA extraction has indicated the existence of a vast diversity of genotypes, but how this relates to functional and phenotypic diversity has not been sufficiently explored. It has been implied that genetic distance per se correlates with phenotypic differentiation and thus reflects subtle (but undiscovered) adaptive fine-tuning to the environment, and that microbes may show biogeographic patterns at the genetic level. Here, we argue that no theoretically based species concept exists; species represent only the basic unit in the taxonomic hierarchy. The significance of naming species is that it organizes biological information. The reason why microbial species collectively represent large genetic differences is owing to huge absolute population sizes, absence of allopatric speciation and low extinction rates. Microbial phenotypes are, therefore, ancient in terms of the geological time-scale and have been maintained through stabilizing selection. These problems are discussed with special reference to eukaryotic micro-organisms.     

Production and efficiency of protozoa

Despite the chronic and debilitative nature of the infection they cause, several species of microsporidia and neogregarines offer a good potential as microbial control agents, particularly against insect pests of high economic thresholds. Techniques for mass production of protozoa have usually involved per os, inoculation or injection of the protozoa into their usual or alternate hosts. The spores are harvested subsequently from heavily infected host tissues by grinding, filtration, and differential centrifugation. Although fresh spores are used in most field tests, the spores of many species can be stored with high survival either frozen or in water at low temperatures (0–4°C) for up to several months. Sunlight or ultraviolet (UV) radiation is a serious factor limiting spore persistence. However, the protozoa do not appear to be significantly limiting spore persistence. However, the protozoa do not appears to be significantly more susceptible to UV radiation than other insect pathogens and persistence can be prolonged with UV protectants. Most field tests with protozoa have involved the application of spores in sprays and have usually resulted in a high degree of infection in the target host species. The potential for control of few species has been improved by formulation of spores in to baits, and the potential of other species will likely increase if suitable bait formulation can be devised in the future. One species, Nosema locustae, formulated as a bait, has been successfully used to control grasshoppers on rangelands. Limited laboratory and field studies have also suggested that increased short-term control might be obtained if candidate protozoan species can be combined with certain insecticides. While recent and increased efforts have been devoted to assess the potential of protozoa as microbial control agents, potential hazards to nontarget organism have been investigated for only three species. Their close relation taxonomically to protozoa pathogenic for mammals will necessitate careful evaluation of the safety of candidate control species for nontarget organisms.     

Inventory and monitoring of wine microbial consortia

The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation, respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity. PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production. Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries, in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified. The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated from very old vintages. B. bruxellensis and O. oeni were the most frequent.     

DNA barcoding to map the microbial communities: current advances and future directions

During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.     

全球变暖背景下土壤微生物呼吸的热适应性:证据、机理和争议

土壤微生物呼吸的热适应性被认为是决定陆地生态系统对全球变暖反馈作用的潜在重要机制,可能显著改变未来的气候变化趋势,然而学术界对于这一机制是否真实存在尚有分歧。阐述了土壤微生物呼吸的热适应性概念,从证据、机理和争议3方面对已有研究进展进行了综述和分析。土壤微生物呼吸的热适应性是微生物在群落尺度上对温度变化的适应性,具有坚实的生物学与生态学理论基础,研究者们运用各类指标已在许多实验中证实土壤微生物物种及群落的呼吸过程能够在高温环境产生适应性变化。土壤微生物呼吸的热适应性机理涉及生物膜结构变化、酶活性变化、微生物碳分配比例变化和微生物群落结构变化等方面。关于土壤微生物呼吸热适应性的争议可能是由研究方法、微生物物种及环境条件的差异引起的。根据对已有研究的分析,认为土壤微生物呼吸的热适应性是真实存在的,未来的研究可进一步探索土壤微生物呼吸的热适应性机理,深入研究环境和全球变化对土壤微生物呼吸的热适应性影响,定量评估土壤微生物呼吸的热适应性对陆地生态系统反馈过程的影响。     

Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts

The human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA-based taxonomic analyses using next-generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 10¹³ microbial cells, NGS read counts are given in multiples of 10⁶, making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as ‘keystone species’, which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host-derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO-mediated microbiota formation in the infant gut.     

Germanium and silver resistance, accumulation, and toxicity in microorganisms.

Germanium is an inert metal with no known biological function in prokaryotic or eukaryotic organisms. Its toxicity is low compared to that of silver. Germanium is accumulated in certain bacterial strains by either energy-independent passive binding or an energy-dependent mechanism. Little is known about the molecular aspects of silver resistance, toxicity, and accumulation in bacterial strains. This is surprising because silver has been used as an antimicrobial agent in the medical field for centuries. It is likely that silver ions are excluded (resulting in decreased silver accumulation) from certain bacterial strains or immobilized intracellularly to prevent toxic effects from being exerted. These mechanisms of silver resistance have not been fully elucidated. This review examines the toxicity and accumulation of germanium and silver in selected microbial species. In addition, resistance mechanisms to these biologically nonessential metals is discussed, with more emphasis placed on silver-resistant bacteria due to the knowledge available.