Intra And Inter Species Interactions In Microbial Communities

Recent developments in various “OMICs” fields have revolutionized our understanding of the vast diversity and ubiquity of microbes in the biosphere. However, most of the current paradigms of microbial cell biology, and our view of how microbes live and what they are capable of, are derived from in vitro experiments on isolated strains. Even the co-culturing of mixed species to interrogate community behavior is relatively new. But the majority of microorganisms lives in complex communities in natural environments, under varying conditions, and often cannot be cultivated. Unless we obtain a detailed understanding of the near-native 3D ultrastructure of individual community members, the 3D spatial community organization, their metabolic interdependences, coordinated gene expression and the spatial organization of their macromolecular machines inventories as well as their communication strategies, we won’t be able to truly understand microbial community life. How spatial and also temporal organization in cell–cell interactions are achieved remains largely elusive. For example, a key question in microbial ecology is what mechanisms microbes employ to respond when faced with prey, competitors or predators, and changes in external factors. Specifically, to what degree do bacterial cells in biofilms act individually or with coordinated responses? What are the spatial extent and coherence of coordinated responses? In addition, networks linking organisms across a dynamic range of physical constraints and connections should provide the basis for linked evolutionary changes under pressure from a changing environment. Therefore, we need to investigate microbial responses to altered or adverse environmental conditions (including phages, predators, and competitors) and their macromolecular, metabolic responses according to their spatial organization. We envision a diverse set of tools, including optical, spectroscopical, chemical and ultrastructural imaging techniques that will be utilized to address questions regarding e.g. intra- and inter-organism interactions linked to ultrastructure, and correlated adaptive responses in gene expression, physiological and metabolic states as a consequence of the alterations of their environment. Clearly strategies for co-evolution and in general the display of adaptive strategies of a microbial network as a response to the altered environment are of high interest. While a special focus will be placed on terrestrial sole-species or mixed biofilms, we are also interested in aquatic systems, biofilms in general and microbes living in symbiosis. In this Research Topic, we wish to summarize and review results investigating interactions and possibly networks between microbes of the same or different species, their co-occurrence, as well as spatiotemporal patterns of distribution. Our goal is to include a broad spectrum of experimental and theoretical contributions, from research and review articles to hypothesis and theory, aiming at understanding microbial interactions at a systems level.

Understand how the intricacies of multispecies community life are related to human oral health. * Explores the immense opportunities presented by readily accessible, genetically tractable, genome-sequenced oral species that naturally form multispecies communities. * Highlights model systems that study oral bacterial interactions, including biofilm growth using saliva as the source of nutrition. * Emphasizes the use of genomic inquiry to probe the human oral microbiome.

Microbial communities play central roles in the development and maintenance of human health and in the functioning of the Earth's ecosystems. The microbial biodiversity of many environments has been thoroughly studied in recent years, yet the dominant processes shaping microbiota assembly remain unresolved. In this thesis, I leverage a bottom-up approach to experimentally build synthetic microbial communities and to test the prevalence of different ecological and evolutionary forces. High-throughput experiments in nanoliter droplets show a wide occurrence of bacterial interactions in the form of one species or consortium affecting the abundance and yield of another species. Positive and negative interactions appear unavoidable in bacterial co-cultures when growth is permitted, with growing bacteria typically facilitating non-growing bacteria. In this thesis, I also show that bacterial interspecies interactions in the C. elegans intestine are mostly competitive and hierarchical. Interestingly, simple two-species microbiotas can predict the composition of three-species and eight-species microbiotas in this nematode. Finally, we found that the importance of interspecies interactions is robust to bacterial strains with and without previous exposure to the C. elegans gut, and to worm mutants with different immune activities. These results show that constructing and characterizing synthetic microbial communities can elucidate fundamental principles for the control of microbial communities.

This book is a treatise on microbial ecology that covers traditional and cutting-edge issues in the ecology of microbes in the biosphere. It emphasizes on study tools, microbial taxonomy and the fundamentals of microbial activities and interactions within their communities and environment as well as on the related food web dynamics and biogeochemical cycling. The work exceeds the traditional domain of microbial ecology by revisiting the evolution of cellular prokaryotes and eukaryotes and stressing the general principles of ecology. The overview of the topics, authored by more than 80 specialists, is one of the broadest in the field of environmental microbiology. The overview of the topics, authored by more than 80 specialists, is one of the broadest in the field of environmental microbiology.

Microbial communities underlie an enormous number of natural processes, yet we have only recently begun to build a predictive understanding of their ecological and evolutionary dynamics. Modeling complex communities requires knowledge of the patterns of ecological interactions and their frequency dependence within and between species. The dearth of available information about the pattern and type of microbial interactions has limited our comprehension of ecological systems and our ability to engineer microbial consortia. Here, I use a variety of approaches to uncover how interactions shape the community and population ecology of a genus of naturally antibiotic producing bacteria, Streptomyces. I find that the outcome of laboratory competitions between strains is often surprisingly sensitive to the initial relative abundance of the strains. Furthermore, I find that even individual cells of the same strain can have dramatically different numbers of descendants after growing together for a short amount of time. Both of these results are linked to inter- and intra-species interactions that may be mediated by antibiotics or other small molecules. Hence, two overarching conclusions are drawn: (i) the importance of frequency dependence in determining the effects of interactions and (ii) that experiments with relatively simple microbial communities can lead to unexpected results. These conclusions have several immediate implications for how we undertake predictive modeling of microbial communities. They indicate that interactions exhibit inherent nonlinearities that predispose the communities to multiple stable states and make developing predictive models more difficult. Also, these results suggest that it is worthwhile to continue developing an understanding of simple microbial communities that can serve as a foundation for models attempting to predict dynamics in communities as complex as those regularly encountered in natural systems.

Recent years have seen tremendous progress in unraveling the molecular basis of different plant-microbe interactions. Knowledge has accumulated on the mecha nisms of the microbial infection of plants, which can lead to either disease or resistance. The mechanisms developed by plants to interact with microbes, whether viruses, bacteria, or fungi, involve events that can lead to symbiotic association or to disease or tumor formation. Cell death caused by pathogen infection has been of great interest for many years because of its association with plant resistance. There appear to be two types of plant cell death associated with pathogen infection, a rapid hypersensitive cell death localized at the site of infection during an incompatible interaction between a resistant plant and an avirulent pathogen, and a slow, normosensitive plant cell death that spreads beyond the site of infection during some compatible interactions involving a susceptible plant and a virulent, necrogenic pathogen. Plants possess a number of defense mechanisms against infection, such as (i) production of phytoalexin, (ii) formation of hydrolases, (iii) accumulation of hydroxyproline-rich glycoprotein and lignin deposition, (iv) production of pathogen-related proteins, (v) produc tion of oligosaccharides, jasmonic acid, and various other phenolic substances, and (vi) production of toxin-metabolizing enzymes. Based on these observations, insertion of a single suitable gene in a particular plant has yielded promising results in imparting resistance against specific infection or disease. It appears that a signal received after microbe infection triggers different signal transduction pathways.

Microbial communities are typically incredibly diverse, with many species contributing to the overall function of the community. The structure of these communities is the result of many complex biotic and abiotic factors. In this thesis, my colleagues and I employ a bottom-up approach to investigate the role of interspecies interactions in determining the structure of multispecies communities. First, we investigate the network of pairwise competitive interactions in a model community consisting of 20 strains of naturally co-occurring soil bacteria. The resulting interaction network is strongly hierarchical and lacks significant non-transitive motifs, a result that is robust across multiple environments. Multispecies competitions resulted in extinction of all but the most highly competitive strains, indicating that higher order interactions do not play a major role in structuring this community. Given the lack of non-transitivity and higher order interactions in vitro, we conclude that other factors such as temporal or spatial heterogeneity must be at play in determining the ability of these strains to coexist in nature. Next, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. These results demonstrate experimentally the ability of a simple bottom-up approach to predict the structure of communities and illuminate the factors that determine their composition.

This book illustrates the importance and significance of Quorum sensing (QS), it’s critical roles in regulating diverse cellular functions in microbes, including bioluminescence, virulence, pathogenesis, gene expression, biofilm formation and antibiotic resistance. Microbes can coordinate population behavior with small molecules called autoinducers (AHL) which serves as a signal of cellular population density, triggering new patterns of gene expression for mounting virulence and pathogenesis. Therefore, these microbes have the competence to coordinate and regulate explicit sets of genes by sensing and communicating amongst themselves utilizing variety of signals. This book descry emphasizes on how bacteria can coordinate an activity and synchronize their response to external signals and regulate gene expression. The chapters of the book provide the recent advancements on various functional aspects of QS systems in different gram positive and gram negative organisms. Finally, the book also elucidates a comprehensive yet a representative description of a large number of challenges associated with quorum sensing signal molecules viz. virulence, pathogenesis, antibiotic synthesis, biosurfactants production, persister cells, cell signaling and biofilms, intra and inter-species communications, host-pathogen interactions, social interactions & swarming migration in biofilms.