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Cellular Dialogues in the Holobiont

When does symbiosis begin? Bacterial cues necessary for metamorphosis in the marine polychaete Hydroides elegans The symbiosis space Chemical cues mediate symbiotic interactions How do specific symbiotic interactions begin? Examples from the pre-symbiosis space Bacterially induced metamorphosis of marine invertebrate animals Bacterial induction of metamorphosis in Hydroides elegans Identification of larval metamorphic cues from biofilm bacteria How variability of inductive bacteria and identified settlement cues relate to variable larval settlement and recruitment Lipopolysaccharide mediates both symbiotic and pre-symbiotic interactions Conclusion References The language of symbiosis: Insights from protist biology Introduction Cytoplasm as microcosm Eukaryotes inside eukaryotes (inside other eukaryotes)Ectosymbiosis: It’s a jungle out there Microbial symbioses: Power struggles in time and space Conclusion Acknowledgments References Trichoplax and its bacteria: How many are there? Are they speaking?Introduction How many symbionts are known to be present and where do they occur?Do all placozoans harbor both G. incantans and R. eludens?Intracellular locations of the placozoan symbionts Unusual mitochondria in placozoan fiber cells and their possible relationship to symbiosis Molecular inferences on the nature of the Trichoplax-bacteria symbioses How are the bacterial symbionts of placozoans transmitted between generations?Some big questions remaining and suggestions for their resolution Acknowledgments References Decoding cellular dialogues between sponges, bacteria, and phages Introduction Host–bacteria dialogue Sponge immune receptors Microbe associated molecular patterns (MAMPs)Bacteria–bacteria dialogue Quorum sensing Quorum quenching Phage-bacteria–host dialogue Phage diversity and host-specificity Ankyphages aid symbionts in immune evasion Conclusions and future perspectives Acknowledgments References Symbiotic interactions in the holobiont Hydra Introduction Interactions between Hydra viridissima and the Chlorella photobiont Location and transmission of the photobiont Mutual benefits Establishment and maintenance of the Chlorella-Hydra symbiosis Molecular mechanisms involved in maintaining the symbiosis Interactions between Hydra and symbiotic bacteria Spatial localization of the bacteria in the Hydra host Bacteria provide protection against fungal infection The innate immune system shapes the host microbiome Crosstalk between innate immunity and stem cell factors Crosstalk between the microbiota and the nervous system Effect of bacteria on host physiology Conclusion: Hydra, an excellent model to understand inter-species interactions Acknowledgments References Hydra and Curvibacter: An intimate crosstalk at the epithelial interface Introduction Hydra and Curvibacter: The ideal duo to understand inter-kingdom communications Spatial localization and transmission of Curvibacter Establishment and carrying capacity of Curvibacter colonization Curvibacter function in the Hydra metaorganism Inter-kingdom communication between Hydra and Curvibacter Outlook Acknowledgments References The coral holobiont highlights the dependence of cnidarian animal hosts on their associated microbes Introduction: The coral holobiont as an ecosystem engineer and its reliance on associated microbes The coral–Symbiodiniaceae relationship Symbiodiniaceae: Micro-algal engines of the coral holobiont machinery Innate immunity, symbiosis sensing, and cell signaling Coral bleaching: The breakdown of the coral–Symbiodiniaceae relationship Symbiodiniaceae–bacteria relationships Diversity and function of microbes associated with the coral host The host as a habitat Diversity of coral-associated bacteria and interspecies interactions Acquisition of bacterial associates and their roles in early coral life-stages Coral probiotics Contribution of bacteria to holobiont nutrient cycling Archaea associated with the coral holobiont Protists and fungi associated with the coral holobiont Summary and Outlook References Extra-intestinal regulation of the gut microbiome: The case of C. elegans TGFß/SMA signaling Introduction: Caenorhabditis elegans as a model for studying the holobiont The C. elegans gut microbiome and the factors that shape it The intestinal niche Host immunity and its role in shaping the intestinal niche Multitissue contributions of TGFß signaling control anterior gut commensal abundance and function TGFß signaling and cell nonautonomous regulation of intestinal function Conclusions and future prospects: Convergence with other systems of host–symbiont interactions Acknowledgments References Multiple roles of bacterially produced natural products in the bryozoan Bugula neritina Introduction Bryozoans, Bugula spp., and Bugula neritina Bryostatins Bryostatin production by the bacterial symbiont of B. neritina Defensive role of bryostatins Impacts of symbiont and symbiont-produced metabolites on host physiology Bryostatins and symbionts in closely related genera Future directions Acknowledgments References The molecular dialogue through ontogeny between a squid host and its luminous symbiont Introduction Features of the Euprymna scolopes-Vibrio fischeri association as a model symbiosis Host activities before symbiont colonization: Embryogenesis and early posthatching Early posthatching activity that mediates species and strain specificity of the association Colonization and early development The basis of a stable symbiosis: Daily rhythms and maturation of the symbiotic organ Conclusions Acknowledgments References Evolving integrated multipartite symbioses between plant-sap feeding insects (Hemiptera) and their endosymbionts Introduction Roles of Hemipteran symbionts: Nutrition and beyond Genome evolution in Hemipteran symbionts Symbiont bearing organs: Transmission and development Intracellular symbioses: Transovarial transmission and bacteriome development Extracellular symbioses: External transmission and the midgut Maintaining and regulating microbial symbionts Evolution of mechanisms to maintain and regulate symbionts Symbiont self-help and self-regulation Symbiont-symbiont support Host support and regulation of nutritional synthesis in symbionts Host support and regulation of other symbiont cell functions Conclusion References Symbiosis for insect cuticle formation Introduction Weevil–Nardonella endosymbiosis Nardonella genome is extremely reduced and specialized for tyrosine synthesis Nardonella endosymbiotic system in Pachyrhynchus infernalis Nardonella-harboring bacteriome as a tyrosine-producing organ Suppression of Nardonella by antibiotic and its effects on tyrosine and DOPA provisioning Contribution of Nardonella to adult cuticle formation in Pachyrhynchus infernalis Incomplete tyrosine synthesis pathway of Nardonella and complementation by host genes Insights from weevil-Nardonella symbiosis: Host’s final step control over symbiont’s metabolic pathway Insights from weevil-Nardonella symbiosis: How do symbiont replacements proceed?Symbiosis for insect cuticle formation: General phenomena across diverse insect taxa Conclusion and perspective Acknowledgments References Microbial determinants of folivory in insects Introduction Deconstructing the plant cell wall Symbiont-mediated evasion of plant defenses Niche preservation Conclusions References Right on cue: Microbiota promote plasticity of zebrafish digestive tract Introduction Development under immune surveillance Developmental plasticity at the luminal interface Beyond the lumen: A secreted bacterial protein impacts pancreas development Conclusions References Uncovering the history of intestinal host–microbiome interactions through vertebrate comparative genomics Introduction A history of symbiotic interactions captured within microbial and host genomes Capturing symbiotic signals within coding regions of the host genome Uncovering specific symbiotic signals in host transcriptional programs Specific symbiotic signals within regulatory regions linked to microbiota-regulated genes Evolutionary conservation of cis-regulatory regions A case study—conserved microbial suppression of Angptl4 Prospectus References Molecular interactions of microbes and the plant phyllosphere: The phyllosphere-microbiome is shaped by the interplay of secreted microbial molecules and the plant immune system Introduction: Multi-partite microbial interactions in the plant phyllosphere The plant immune system as a microbial management system Do pattern recognition receptors (PRRs) direct microbiota assembly?Do intra-cellular NLR proteins contribute to assembly of microbial consortia?Interactions of plant pathogens and the plant microbiota: Systemic effects in susceptible and resistant plants Microbial effectors mediate plant-microbe interactions Perspective Acknowledgments References Cellular dialogues between hosts and microbial symbionts: Generalities emerging

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