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This chapter investigates the different definitions of immunology, in particular the dominant definition stating that immunology is the discipline that studies the defense of organisms against pathogens. The different steps towards the autonomy of immunology as a discipline are examined, from immunization to the elaboration of a theory of immunity, and eventually the institutionalization of the domain. I propose my own definition of immunology as the discipline that studies specific interactions between immune receptors and antigenic patterns, triggering mechanisms that destroy or prevent the destruction of target antigens. I show that, contrary to what has long been believed, every organism has an immune system. I describe several examples of immune systems (in mammals, insects, plants, and even unicellulars). I close this chapter by an analysis of the concepts generally considered as central in immunology, those of “self” and “nonself.”

This chapter offers a critique of the self-nonself theory. I first analyze data on autoreactivity and normal autoimmunity, in particular phagocytosis and regulatory cells, in order to reject the idea that self constituents do not trigger immune responses. In a second step, thanks to a description of immune tolerance to genetically foreign entities, including the fetus and huge amounts of commensal and symbiotic bacteria, I reject the idea that every nonself triggers an immune response of rejection. I show that every organism is “impure” in so far as it contains a great number of “nonself” constituents. I conclude that the self-nonself theory is experimentally inadequate, and conceptually too vague to still be used as a satisfying scientific framework to explain the triggering of immune responses.

This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis-Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about 10-fold smaller than the equivalent spherical diameter of the protistan predator. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world, and are critical links between microbial food chains and larger organisms. Many protists, especially in aquatic habitats, are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested, photosynthetic prey or its chloroplasts.

The opportunity for arms-race evolution between host and pathogens is one reason why genes involved in immune functions are often rapidly evolving. Innate immune systems lack the degree of pathogen specificity that makes such arms races easy to initiate, but nevertheless they too harbour rapidly evolving genes. While core signalling genes retain one-to-one orthology, both recognition and antimicrobial peptide genes display rapid changes in copy number. With respect to turnover of amino acids in the proteins themselves, receptors that are involved in phagocytosis evolve the fastest, with signalling proteins also evolving rapidly as a consequence of microbial attack. Antimicrobial peptides have a comparatively slow rate of amino acid replacement. Finally, several proteins involved in viral and transposon defence are exceptionally rapid in their evolutionary rates, possibly as a consequence of an arms race process whose rate is driven by the high mutation rate of viruses.

Textbooks on immunology rarely spend more than a few pages describing the principles of invertebrate immunology. Coming away from these often gives the reader the impression that this immune system is simple and non-specific in nature yet with over 1.3 million extant species of invertebrates, there is inevitably a great diversity of strategies to defend against disease. Furthermore, invertebrates have unique mechanisms of defence including the prophenoloxidase system only found in arthropods, molluscs, echinoderms and tunicates and some forms of ‘acquired’ immunity where the host has an apparent specific heightened response on second exposure to a parasite or pathogen. This chapter aims to provide a concise overview of the broad invertebrate defence mechanisms to parasites and pathogens, and how such agents can overcome and/or circumvent these defences to cause disease.

Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.