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A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit. The components of a holobiont are individual species or bionts, while the combined genome of all bionts is the hologenome. The concept of the holobiont was defined by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation. Holobionts include the host, virome, microbiome, and other members, all of which contribute in some way to the function of the whole. Well-studied holobionts include reef-building corals and humans.
A holobiont is a collection of species that are closely associated and have complex interactions, such as a plant species and the members of its microbiome. Each species present in a holobiont is a biont, and the genomes of all bionts taken together is the hologenome, or the "comprehensive gene system" of the holobiont. A holobiont typically includes a eukaryote host and all of the symbiotic viruses, bacteria, fungi, etc. that live on or inside it.
Holobionts are distinct from superorganisms; superorganisms are consist of many individuals, sometimes of the same species, and is commonly applied to eusocial insects. An ant colony can be described as a superorganism while an individual ant and its associated bacteria, fungi, etc. is a holobiont. However, there is still some controversy surrounding these terms, and they have been used interchangeably in some publications.
Components of the Holobiont
Reef-building corals are holobionts that include the coral itself (a eukaryotic invertebrate within class Anthozoa), photosynthetic dinoflagellates called zooxanthellae (Symbiodinium), and associated bacteria and viruses.
The plant holobiont is relatively well-studied, with particular focus on agricultural species such as legumes and grains. Bacteria, fungi, archaea, protists, and viruses are all members of the plant holobiont.
The bacteria phyla known to be part of the plant holobiont are Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria . For example, nitrogen-fixers such as Azotobacter (Proteobacteria) and Bacillus (Firmicutes) greatly improve plant performance.
Fungi of the phyla Ascomycota, Basidiomycota, and Glomeromycota colonize plant tissues and provide a variety of functions for the plant host. Arbuscular mycorrhizal fungi (Glomeromycota), for instance, are common across plant groups and provide improved nutrient acquisition, temperature and drought resistance, and reduced pathogen load. Epichloë species (Ascomycota) are part of the meadow fescue holobiont and provide herbivore resistance by producing ergot alkaloids, which cause ergotism in mammals.
Protist members of the plant holobiont are less well-studied, with most knowledge oriented towards pathogens. However, there are examples of commensalistic plant-protist associations, such as Phytomonas (Trypanosomatidae).
Some authors reject the holobiont concept, saying it does not sufficiently encompass the intricacies of host-symbiont relationships.
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