Inter And Intra Species Cooperation In Natural And Synthetic 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.

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.

By investigating a simple question, a philosopher of science and a molecular biologist offer an accessible understanding of microbial communities and a motivating theory for future research in community ecology. Microorganisms, such as bacteria, are important determinants of health at the individual, ecosystem, and global levels. And yet many aspects of modern life, from the overuse of antibiotics to chemical spills and climate change, can have devastating, lasting impacts on the communities formed by microorganisms. Drawing on the latest scientific research and real-life examples such as attempts to reengineer these communities through microbial transplantation, the construction of synthetic communities of microorganisms, and the use of probiotics, this book explores how and why communities of microorganisms respond to disturbance, and what might lead to failure. It also unpacks related and interwoven philosophical questions: What is an organism? Can a community evolve by natural selection? How can we make sense of function and purpose in the natural world? How should we think about regeneration as a phenomenon that occurs at multiple biological scales? Provocative and nuanced, this primer offers an accessible conceptual and theoretical understanding of regeneration and evolution at the community level that will be essential across disciplines including philosophy of biology, conservation biology, microbiomics, medicine, evolutionary biology, and ecology.

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.

Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.

The most evident aspect of biodiversity is the variety of complex forms and behaviors among organisms, both living and extinct. Comparative molecular and physiological studies show that the evolution of complex phenotypic traits involves multiple levels of biological organization (i.e. genes, chromosomes, organelles, cells, individual organisms, species, etc.). Regardless of the specific molecular mechanisms and details, the evolution of different complex biological organizations share a commonality: cooperation and conflict among the parts of the biological unit under study. The potential for conflict among parts is abundant. How then do complex systems persist, given the necessity of cooperative behavior for their maintenance, when the potential for conflict occurs across all levels of biological organization? In this Research Topic and eBook we present ideas and work on the question, how coexistence of biological components at different levels of organization persists in the face of antagonistic, conflicting or even exploitative behavior of the parts? The goal of this topic is in presenting examples of cooperation and conflict at different levels of biological organization to discuss the consequences that this “tension” have had in the diversification and emergence of novel phenotypic traits. Exemplary cases are studies investigating: the evolution of genomes, formation of colonial aggregates of cells, biofilms, the origin and maintenance of multicellular organisms, and the stable coexistence of multispecies consortia producing a cooperative product. Altogether, we hope that the contributions to this Research Topic build towards mechanistic knowledge of the biological phenomenon of coexistence in the face of conflict. We believe that knowledge on the mechanisms of the origin and evolutionary maintenance of cooperation has implications beyond evolutionary biology such as novel approaches in controlling microbial infections in medicine and the modes by studies in synthetic biology are conducted when designing economically important microbial consortia.

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.

Biochemistry and ecology of biofilms from industrial, medical and other viewpoints.