User:Popcorntea/Holobiont

A holobiont is an assemblage of a host and the 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.

Definition
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.

Versus Superorganism
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; an individual ant and its associated bacteria, fungi, viruses, etc. is a holobiont. However, there is still some confusion surrounding these terms, and they have been used interchangeably in some publications.

Host
The host member of a holobiont is typically a multicellular eukaryote, such as a plant or human. Notable hosts that are well-studied include humans, corals , and pine trees.

Virome
All of the viruses included in a holobiont are collectively referred to as the virome.

Microbiome
The microbiome includes bacteria, archaea , microscopic fungi , and microscopic protists.

Other bionts
Multicellular fungi can be included in holobionts, such as arbuscular mycorrhizal fungi (AMF) in the roots of plants. Small insects such as mites can also fall into this category.

In plants
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).

Criticism
Some authors reject the holobiont concept as they believe it does not sufficiently encompass the myriad of host-symbiont relationships to make it justifiable. They would also argue that symbionts do not necessarily co-evolve with the host.