The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium

Traditionally microorganisms were considered to be autonomous organisms that could be studied in isolation. However, over the last decades cell-to-cell communication has been found to be ubiquitous. By secreting molecular signals in the extracellular environment microorganisms can indirectly assess the cell density and respond in accordance. In one of the best-studied microorganisms, Bacillus subtilis, the differentiation processes into a number of distinct cell types have been shown to depend on cell-to-cell communication. One of these cell types is the spore. Spores are metabolically inactive cells that are highly resistant against environmental stress. The onset of sporulation is dependent on cell-to-cell communication, as well as on a number of other environmental cues. By using individual-based simulations we examine when cell-to-cell communication that is involved in the onset of sporulation can evolve. We show that it evolves when three basic premises are satisfied. First, the population of cells has to affect the nutrient conditions. Second, there should be a time-lag between the moment that a cell decides to sporulate and the moment that it turns into a mature spore. Third, there has to be environmental variation. Cell-to-cell communication is a strategy to cope with environmental variation, by allowing cells to predict future environmental conditions. As a consequence, cells can anticipate environmental stress by initiating sporulation. Furthermore, signal production could be considered a cooperative trait and therefore evolves when it is not too costly to produce signal and when there are recurrent colony bottlenecks, which facilitate assortment. Finally, we also show that cell-to-cell communication can drive ecological diversification. Different ecotypes can evolve and be maintained due to frequency-dependent selection.     

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。     

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.     

Toward an understanding of microbial communities through analysis of communication networks

Bacteria receive signals from diverse members of their biotic environment. They sense their own species through the process of quorum sensing, which detects the density of bacterial cells and regulates functions such as bioluminescence, virulence, and competence. Bacteria also respond to the presence of other microorganisms and eukaryotic hosts. Most studies of microbial communication focus on signaling between the microbe and one other organism for empirical simplicity and because few experimental systems offer the opportunity to study communication among various types of organisms. But in the real biological world, microorganisms must carry on multiple molecular conversations simultaneously between diverse organisms, thereby constructing communication networks. We propose that biocontrol of plant disease, the process of suppressing disease through application of a microorganism, offers a model for the study of communication among multiple organisms. Successful biocontrol requires the sending and receiving of signals between the biocontrol agent and the pathogen, plant host, and microbial community surrounding the host. We are using Bacillus cereus, a biocontrol agent, and the organisms it must interact with, to dissect a communication network. This system offers an excellent starting point for study because its members are defined and well studied. An understanding of signaling in the B. cereus biocontrol system may provide a model for network communication among organisms that share a habitat and provide a new angle of analysis for understanding the interconnections that define communities. This revised version was published online in August 2006 with corrections to the Cover Date.     

共生微生物对昆虫化学感受的影响北大核心

共生微生物通过影响昆虫信息化合物的合成或感受来调控宿主的化学通讯,进而影响昆虫的交流、防御、捕食和扩散行为。这种调控作用有助于共生微生物的扩散,但对宿主可能是有利的,也可能是有害的,并为共生体系的协同进化提供动力。本文围绕近年来共生微生物对昆虫化学感受的影响及其机制展开综述,并分析其进化意义,旨在为昆虫化学生态学理论提供补充,并为开发新的害虫防治策略提供思路。     

Probiotics and Psychobiotics: the Role of Microbial Neurochemicals

Probiotics and Antimicrobial Proteins - In light of recent data, microorganisms should be construed as organisms that are capable of communication and collective behaviors. Microbial communication...     

Conceptualizing "suicidal genetically engineered microorganisms" for bioremediation applications

Use of genetically modified microorganisms (GEMs) for pollution abatement has been limited because of risks associated with their release in the environment. Recent developments in the area of recombinant DNA technologies have paved the way for conceptualizing "suicidal genetically engineered microorganisms" (S-GEMS) to minimize such anticipated hazards and to achieve efficient and safer bioremediation of contaminated sites. Our strategy of designing a novel S-GEM is based on the knowledge of killer-anti-killer gene(s) that would be susceptible to programmed cell death after detoxification of any given contaminated site(s).     

废水处理中群体感应调控行为研究进展

群体感应是微生物在繁殖过程中分泌一些特定的信号分子,当信号分子浓度达到一定阈值后,可以调控某些基因表达,从而实现信息交流的现象.群体感应调控着生物膜形成、公共物质合成、基因水平转移等一系列社会性行为,广泛存在于各类微生物信息交流中.活性污泥、生物膜和颗粒污泥等生物聚集体广泛存在群体感应现象,了解和认识群体感应与微生物之间的调控行为,对于废水处理具有重要意义.本文综述了感应信号分子的分类、群体感应调控机制,群体感应在活性污泥、生物膜、好氧颗粒污泥和厌氧颗粒污泥等废水处理中的调控行为的研究进展,并对废水处理中群体感应的研究进行了展望,以期为深入理解废水处理中群体感应调控行为提供参考.     

藻际环境中微生物胞间通讯行为及作用

藻际环境中,微生物通过营养物质交换和活性物质释放相互作用,进而引发共生、竞争或合作等行为.结合环境条件的影响,藻际环境一般具有稳定而多样的微生态结构.以上行为发生的基础是以信号分子为媒介的微生物胞间通讯作用.本文系统综述了藻际环境的特征、藻际胞间通讯行为以及藻际胞间信号分子的类别与作用机制.特别针对痕量信号分子特性,结...     

Database on natural and transgenic luminous microorganisms: "BiolumBase"

The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with lux genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.     

On the origin of prokaryotic "species": the taxonomy of halophilic Archaea

The consistent use of the taxonomic system of binomial nomenclature (genus and species) was first popularized by Linnaeus nearly three-hundred years ago to classify mainly plants and animals. His main goal was to give labels that would ensure that biologists could agree on which organism was under investigation. One-hundred fifty years later, Darwin considered the term species as one of convenience and not essentially different from variety. In the modern era, exploration of the world's niches together with advances in genomics have expanded the number of named species to over 1.8 million, including many microorganisms. However, even this large number excludes over 90% of microorganisms that have yet to be cultured or classified. In naming new isolates in the microbial world, the challenge remains the lack of a universally held and evenly applied standard for a species. The definition of species based on the capacity to form fertile offspring is not applicable to microorganisms and 70% DNA-DNA hybridization appears rather crude in light of the many completed genome sequences. The popular phylogenetic marker, 16S rRNA, is tricky for classification since it does not provide multiple characteristics or phenotypes used classically for this purpose. Using most criteria, agreement may usually be found at the genus level, but species level distinctions are problematic. These observations lend credence to the proposal that the species concept is flawed when applied to prokaryotes. In order to address this topic, we have examined the taxonomy of extremely halophilic Archaea, where the order, family, and even a genus designation have become obsolete, and the naming and renaming of certain species has led to much confusion in the scientific community.     

Decision making in the NICU--strategies,statistics, and "satisficing"

As science progresses, new issues in bioethics grab the headlines, but in neonatal medicine communication and decision making for sick and premature infants is as important today as it was thirty years ago. Decisions have to be made and made well, despite suboptimal time, data, or knowledge. To this end, the authors propose good communication and a cooperative model as key to interpreting the best interest standard in a way that respects parental rights and responsibility and allows best interest to be decided from an amalgam of medical facts and human values.     

“微生物-肠-脑”轴介导的宿主食欲调节

人和动物的食欲受到中枢神经系统和外周激素的协同调控。近年来，一些研究指出肠道菌群的组成与变化通过多重途径影响宿主的食欲。肠道细菌分泌和产生的大量功能性代谢物如短链脂肪酸、次级胆汁酸和氨基酸衍生物等是其发挥调控作用的重要媒介物质。此外，肠道菌群还能够影响消化系统营养感知、肠迷走神经信号投递、肠道激素分泌等，这些也都会参与食欲和进食调节。在明确细菌调控食欲的作用机制后靶向调控和重组肠道微生物可能是改善宿主食欲的一种新策略，有助于厌食症、暴食症等相关疾病的诊治。     

The "most wanted" taxa from the human microbiome for whole genome sequencing

The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP's 16S data sets to several reference 16S collections to create a 'most wanted' list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the 'most wanted', and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the 'most wanted' organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.     

On the estimation of average shear rate in bubble columns

Development of bioengineering using such biomaterials as plant tissues or genetically produced microorganisms makes it important to accurately estimate the prevailing shear rate in bioreactors because they are generally sensitive to shear. Various authors have discussed ways to estimate the average shear rate in a bubble column or an airlift reactor.(1) This communication will explain the background consideration for the development of the expression as gamma(av) = 50 u(g) by the present authors, and give suggestions for further discussions.     

Synthesis of microbial signaling molecules and their stereochemistry-activity relationships

Microbial signaling molecules such as autoinducers and microbial hormones play important roles in intercellular communication in microorganisms. Information transfer between the individual cells of a microorganism is one of the most important biological events among them. Researchers often suffer from extremely low levels of microbial signaling molecule contents, which prevent them from understanding chemistry and biology of intercellular communication in microorganisms. Chemical synthesis is a powerful tool to obtain sufficient amounts of sample and to clarify the structure of a molecule. This review focuses on the synthesis and stereochemistry-bioactivity relationships of five microbial signaling molecules, Vibrio cholerae autoinducer-1 (CAI-1), AI-2 precursor (DPD), an acylhomoserine lactone from Rhizobium leguminosarum (small bacteriocin), a diffusible extracellular factor of Xanthomondas campestris pv. campestris, and Phytophthora mating hormone α1.     

Extension temperature of 60°C required for PCR amplification of large DNA fragments (>5 kb) from a low GC bacterium Clostridium acetobutylicum

PCR amplification of DNA fragments has been routinely used in gene cloning and engineering of microbial strains for biotechnological purposes such as production of biofuels and green chemicals. However, it is often a challenge to amplify large DNA fragments (>5 kb) from low GC microorganisms using the standard PCR protocols. In this brief communication, we report a modified PCR method with an extension temperature of 60°C, which efficiently amplified a 5.3 and a 5.5 kb DNA fragment (an extension time of 6 min) from a low GC bacterium Clostridium acetobutylicum (~30% GC). A lower than normal extension temperature (72°C) approach may also facilitate PCR amplification of large DNA fragments (>5 kb) from other low GC microorganisms.     

Control of microbial attachment by inhibition of ATP and ATP‐mediated autoinducer‐2

In this study, 2,4‐dinitrophenol (DNP), a typical chemical uncoupler, was employed to investigate the possible roles of ATP and autoinducer‐2 (AI‐2) of suspended microorganisms in attachment onto nylon membrane and glass slide surfaces. Results showed that DNP could disrupt ATP synthesis, subsequently led to a reduced production of AI‐2 which is a common signaling molecule for cellular communication. Attachment of suspended microorganisms exposed to DNP was significantly suppressed as compared to microorganisms without contact with DNP. These suggest that an energized state of suspended microorganisms would favor microbial attachment to both nylon membrane and glass slide surfaces. The extent of microbial attachment was found to be positively related to the AI‐2 content of microorganisms. This study offers insights into the control of biofouling by preventing initial microbial attachment through inhibition of energy metabolism. Biotechnol. Bioeng. 2010;107: 31–36. © 2010 Wiley Periodicals, Inc.