Saltational symbiosis

Symbiosis has long been associated with saltational evolutionary change in contradistinction to gradual Darwinian evolution based on gene mutations and recombination between individuals of a species, as well as with super-organismal views of the individual in contrast to the classical one-genome: one organism conception. Though they have often been dismissed, and overshadowed by Darwinian theory, suggestions that symbiosis and lateral gene transfer are fundamental mechanisms of evolutionary innovation are borne out today by molecular phylogenetic research. It is time to treat these processes as central principles of evolution.     

Divining the Essence of Symbiosis: Insights from the Squid-Vibrio Model

Biology has a big elephant in the room. Researchers are learning that microorganisms are critical for every aspect of the biosphere''s health. Even at the scale of our own bodies, we are discovering the unexpected necessity and daunting complexity of our microbial partners. How can we gain an understanding of the form and function of these “ecosystems” that are an individual animal? This essay explores how development of experimental model systems reveals basic principles that underpin the essence of symbiosis and, more specifically, how one symbiosis, the squid-vibrio association, provides insight into the persistent microbial colonization of animal epithelial surfaces.     

Characterization and Function of the First Antibiotic Isolated from a Vent Organism: The Extremophile Metazoan Alvinella pompejana

The emblematic hydrothermal worm Alvinella pompejana is one of the most thermo tolerant animal known on Earth. It relies on a symbiotic association offering a unique opportunity to discover biochemical adaptations that allow animals to thrive in such a hostile habitat. Here, by studying the Pompeii worm, we report on the discovery of the first antibiotic peptide from a deep-sea organism, namely alvinellacin. After purification and peptide sequencing, both the gene and the peptide tertiary structures were elucidated. As epibionts are not cultivated so far and because of lethal decompression effects upon Alvinella sampling, we developed shipboard biological assays to demonstrate that in addition to act in the first line of defense against microbial invasion, alvinellacin shapes and controls the worm''s epibiotic microflora. Our results provide insights into the nature of an abyssal antimicrobial peptide (AMP) and into the manner in which an extremophile eukaryote uses it to interact with the particular microbial community of the hydrothermal vent ecosystem. Unlike earlier studies done on hydrothermal vents that all focused on the microbial side of the symbiosis, our work gives a view of this interaction from the host side.     

Pathogen persistence in infectious pathology

Problems of microorganism's persistence in infectious pathology are discussed in this work. Persistence of bacteria as the form of procaryotic and eucaryotic cells symbiosis unlimitedly long coexistence is considered. Questions of the microbial evolution formed in constant collision of the infective agent with macroorganism defense mechanisms are discussed. The spectrum of known mechanisms bacterial survival in conditions of an infected organism is considered. For discussion the problem of microbial persistence it is offered to include as model alongside with an independent cell, a microbial population as complex self-organizing system--the original "superorganism" having universal chemical regulation, the determining density of a population and equation of some physiological functions. It is offered to consider the host colonization resistance as a phenomenon of general biology directed on maintenance of a microecological homeostasis as a result of symbiotic interactions of an organism and it autochthonous microflora with the "key" kinds of biotope protection. The use of persistence characteristics of microorganisms is proved as a target in conditions of intermicrobial interaction of its allochthonous and autochthonous microflorae. Practical value of such approach in infectious pathology is shown.     

Persistence of bacterial pathogens as a physiological phenomenon

The complex ecosystem of humans and microbes has been presented as an associative symbiosis based on a mutual support of symbionts with different consequences for them. Conditions for the persistence of bacteria have been defined: their resistance to environmental factors, antagonism in biocenosis, and stability to withstand host defense mechanisms. The key role of bacterial peptidoglycan has been defined for their survival in an infected organism, and the classification for persistent mechanisms of pathogens has been given. The group of bacterial secreted protease providing microbial resistance to defense factors of the organism has been described. Host colonizing resistance has been presented as a physiological regulatory system controlling bacterial penetration into an organism. Regulatory mechanisms for bacterial persistence have been discussed.     

Genetic-evolutionary basis of symbiosis doctrine

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.     

The structure of microbial evolutionary theory

The study of microbial phylogeny and evolution has emerged as an interdisciplinary synthesis, divergent in both methods and concepts from the classical evolutionary biology. The deployment of macromolecular sequencing in microbial classification has provided a deep evolutionary taxonomy hitherto deemed impossible. Microbial phylogenetics has greatly transformed the landscape of evolutionary biology, not only in revitalizing the field in the pursuit of life's history over billions of years, but also in transcending the structure of thought that has shaped evolutionary theory since the time of Darwin. A trio of primary phylogenetic lineages, along with the recognition of symbiosis and lateral gene transfer as fundamental processes of evolutionary innovation, are core principles of microbial evolutionary biology today. Their scope and significance remain contentious among evolutionists.     

Molecular microbiology of gut bacteria: genetic diversity and community structure analysis

Recently developed molecular biology approaches make possible the detailed genetic, taxonomic and ecological examination of microorganisms from various habitats. Animal gut represents one of the most complex microbial ecosystems with a large degree of microbial biodiversity present. Bacteria inhabiting the gut usually play important roles in metabolic transformations of substrates and sometimes, e.g. in ruminants, they make the basis for an obligate symbiosis with the host. Here we discuss molecular microbiology as a strategy for examination of gut bacteria, concentrating on a typical and in such environment dominant group of strictly anaerobic Gram-negative bacteria from the phylogenetic group Cytophaga/Flexibacter/Bacteroides. The bacteria from the genus Prevotella are the most abundant Gram-negative bacteria in the rumen and form a distinctive phylogenetic cluster, clearly separated from prevotellas isolated from other ecological niches. They may represent a good choice for a model organism in genetic manipulation experiments and for studies of gene transfer mechanisms taking place in the gut. The molecular tools for detection and monitoring of ruminal prevotellas are discussed.     

The roles of NO in microbial symbioses

Because of its unique chemical properties, nitric oxide (NO) is a pluripotent signalling and effector molecule that is implicated in a variety of biological roles. Although NO is known to function in host innate immunity against pathogen invasion, its possible roles in microbial symbioses with animal and plant hosts remain relatively less well defined. In this review, we discuss the mechanisms by which bacteria sense and/or detoxify NO. We then focus specifically on its roles in microbial symbioses of diverse eukaryotic hosts. Using the squid-vibrio light-organ symbiosis as a well-characterized example, we discuss the ways in which NO serves as a signal, antioxidant and specificity determinant in this model symbiosis. Because beneficial microbial associations are older and much more prevalent than pathogenic ones, it seems likely that the former may be evolutionary precursors of the latter. Thus, knowledge of the roles played by NO in mutualisms will provide insights into its function in disease interactions as well.     

Commentary: Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome

Human beings have co-evolved with the microorganisms in our environment for millions of years, and have developed into a symbiosis in a mutually beneficial/defensive way. Human beings have significant multifaceted relationships with the diverse microbial community. Apart from the important protective role of microbial community exposure in development of early immunity, millions of inimitable bacterial genes of the diverse microbial community are the indispensable source of essential nutrients like essential amino acids and essential fatty acids for human body. The essential nutrition from microbiome is harvested through xenophagy. As an immune effector, xenophagy will capture any microorganisms that touch the epithelial cells of our gastrointestinal tract, degrade them and turn them into nutrients for the use of our body.     

共生概念发展的历史,现状及展望

本文从回顾历史出发,勾划出国际上极为热门的共生学说发展轨迹,指出共生是一切群体中密切联合的能力,不但是诸多生命分支科学的理论网络,涉及到许多应用问题,而且是一种生物哲学,自然界和人文科学莫不如此。     

Plant–Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics‐based technologies has broadened our understanding of the molecular aspects of beneficial plant–microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis‐specific and symbiosis‐related proteins and post‐translational modifications that play a critical role in mediating symbiotic plant–microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other “omics” data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis‐based “omic” approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant‐associated microbial communities is also discussed.     

Host–microbial symbiosis in the mammalian intestine: exploring an internal ecosystem

The mammalian intestine contains a complex, dynamic, and spatially diversified society of nonpathogenic bacteria. Very little is known about the factors that help establish host-microbial symbiosis in this open ecosystem. By introducing single genetically manipulatable components of the microflora into germfree mice, simplified model systems have been created that will allow conversations between host and microbe to be heard and understood. Other paradigms of host–microbial symbiosis suggest that these interactions will involve an exchange of biochemical signals between host and symbionts as well as among the bacteria themselves. The integration of molecular microbiology, cell biology, and gnotobiology should provide new insights about how we adapt to a microbial world and reveal the roles played by our indigenous ‘nonpathogenic’ flora. BioEssays 20 :336-343, 1998. © 1998 John Wiley & Sons, Inc.     

The Microbiota,Chemical Symbiosis,and Human Disease

Our understanding of mammalian–microbial mutualism has expanded by combing microbial sequencing with evolving molecular and cellular methods, as well as unique model systems. Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments—nasal, lung, and gastrointestinal tract—is reviewed with a focus on new knowledge about the taxa, species, proteins, and chemistry that promote health and impact progression toward disease. The information presented is further organized by specific diseases now associated with the microbiota: Staphylococcus aureus infection and rhinosinusitis in the nasal-sinus mucosa, as well as cystic fibrosis, chronic obstructive pulmonary disorder, and asthma in the pulmonary tissues. For the vast and microbially dynamic gastrointestinal compartment, several disorders are considered, including obesity, atherosclerosis, Crohn's disease, ulcerative colitis, drug toxicity, and even autism. Our appreciation of the chemical symbiosis ongoing between human systems and the microbiota continues to grow and suggests new opportunities for modulating this symbiosis using designed interventions.     

A new mathematical model of the dynamics of an age cohort population

A new generalized conception of an organism is given. Based on this conception, a new mathematical model of ontogenesis of an individual and the survival of the age cohort of population was proposed. By using real data on the dynamics of the survival of the age cohort of population, the model enables one to determine the parameters characterizing the relationship man-environment in the context of survival and calculate the dynamics (from birth to death) of the model variables of the state of the organism.     

Developmental symbiosis facilitates the multiple origins of herbivory

Developmental bias toward particular evolutionary trajectories can be facilitated through symbiosis. Organisms are holobionts, consisting of zygote‐derived cells and a consortia of microbes, and the development, physiology, and immunity of animals are properties of complex interactions between the zygote‐derived cells and microbial symbionts. Such symbionts can be agents of developmental plasticity, allowing an organism to develop in particular directions. This plasticity can lead to genetic assimilation either through the incorporation of microbial genes into host genomes or through the direct maternal transmission of the microbes. Such plasticity can lead to niche construction, enabling the microbes to remodel host anatomy and/or physiology. In this article, I will focus on the ability of symbionts to bias development toward the evolution of herbivory. I will posit that the behavioral and morphological manifestations of herbivorous phenotypes must be preceded by the successful establishment of a community of symbiotic microbes that can digest cell walls and detoxify plant poisons. The ability of holobionts to digest plant materials can range from being a plastic trait, dependent on the transient incorporation of environmental microbes, to becoming a heritable trait of the holobiont organism, transmitted through the maternal propagation of symbionts or their genes.     

Nasonia–microbiome associations: a model for evolutionary hologenomics research

In recent years, with the development of microbial research technologies, microbiota research has received widespread attention. The parasitoid wasp genus Nasonia is a good model organism for studying insect behavior, development, evolutionary genetics, speciation, and symbiosis. This review describes key advances and progress in the field of the Nasonia–microbiome interactions. We provide an overview of the advantages of Nasonia as a model organism for microbiome studies, list research methods to study the Nasonia microbiome, and discuss recent discoveries in Nasonia microbiome research. This summary of the complexities of Nasonia–microbiome relationships will help to contribute to a better understanding of the interactions between animals and their microbiomes and establish a clear research direction for Nasonia–microbiome interactions in the future.     

The metaphysics of brain death

The dominant conception of brain death as the death of the whole brain constitutes an unstable compromise between the view that a person ceases to exist when she irreversibly loses the capacity for consciousness and the view that a human organism dies only when it ceases to function in an integrated way. I argue that no single criterion of death captures the importance we attribute both to the loss of the capacity for consciousness and to the loss of functioning of the organism as a whole. This is because the person or self is one thing and the human organism is another. We require a separate account of death for each. Only if we systematically distinguish between persons and human organisms will we be able to provide plausible accounts both of the conditions of our ceasing to exist and of when it is that we begin to exist. This paper, in short, argues for a form of mind-body dualism and draws out some of its implications for various practical moral problems.     

Review: the Antarctic Chlamydomonas raudensis: an emerging model for cold adaptation of photosynthesis

Permanently cold habitats dominate our planet and psychrophilic microorganisms thrive in cold environments. Environmental adaptations unique to psychrophilic microorganisms have been thoroughly described; however, the vast majority of studies to date have focused on cold-adapted bacteria. The combination of low temperatures in the presence of light is one of the most damaging environmental stresses for a photosynthetic organism: in order to survive, photopsychrophiles (i.e. photosynthetic organisms adapted to low temperatures) balance temperature-independent reactions of light energy capture/transduction with downstream temperature-dependent metabolic processes such as carbon fixation. Here, we review research on photopsychrophiles with a focus on an emerging model organism, Chlamydomonas raudensis UWO241 (UWO241). UWO241 is a psychrophilic green algal species and is a member of the photosynthetic microbial eukaryote community that provides the majority of fixed carbon for ice-covered lake ecosystems located in the McMurdo Dry Valleys, Antarctica. The water column exerts a range of environmental stressors on the phytoplankton community that inhabits this aquatic ecosystem, including low temperatures, extreme shade of an unusual spectral range (blue-green), high salinity, nutrient deprivation and extremes in seasonal photoperiod. More than two decades of work on UWO241 have produced one of our most comprehensive views of environmental adaptation in a cold-adapted, photosynthetic microbial eukaryote.