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The root microbiome (also called rhizosphere microbiome) is the dynamic
community A community is a social unit (a group of living things) with commonality such as place, norms, religion, values, customs, or identity. Communities may share a sense of place situated in a given geographical area (e.g. a country, village, tow ...
of
microorganisms A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
associated with plant
root In vascular plants, the roots are the organs of a plant that are modified to provide anchorage for the plant and take in water and nutrients into the plant body, which allows plants to grow taller and faster. They are most often below the sur ...
s. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
,
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
and
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
. The microbial communities inside the root and in the
rhizosphere The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microor ...
are distinct from each other, and from the microbial communities of bulk
soil Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Some scientific definitions distinguish ''dirt'' from ''soil'' by restricting the former te ...
, although there is some overlap in
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...
composition. Different microorganisms, both beneficial and harmful affect development and physiology of plants. Beneficial microorganisms include bacteria that fix nitrogen, promote plant growth, mycorrhizal fungi, mycoparasitic fungi, protozoa and certain biocontrol microorganisms. Pathogenic microorganisms also span certain bacteria, pathogenic fungi and certain nematodes that can colonize the rhizosphere. Pathogens are able to compete with protective microbes and break through innate plant defense mechanisms. Apart from microbes that cause plant diseases, certain bacteria that are pathogenic and can be carried over to humans, such as ''
Salmonella ''Salmonella'' is a genus of rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type species and is fur ...
'', enterohaemorhagic ''Escherichia coli'', '' Burkholedria (ceno)cepacia'', ''
Pseudomonas aeruginosa ''Pseudomonas aeruginosa'' is a common encapsulated, gram-negative, aerobic–facultatively anaerobic, rod-shaped bacterium that can cause disease in plants and animals, including humans. A species of considerable medical importance, ''P. aerugi ...
'', and ''
Stenotrophomonas maltophilia ''Stenotrophomonas maltophilia'' is an aerobic, nonfermentative, Gram-negative bacterium. It is an uncommon bacterium and human infection is difficult to treat. Initially classified as ''Bacterium bookeri'', then renamed ''Pseudomonas maltophil ...
'' can also be detected in root associated microbiome and in plant tissues. Root microbiota affect plant
host A host is a person responsible for guests at an event or for providing hospitality during it. Host may also refer to: Places * Host, Pennsylvania, a village in Berks County People *Jim Host (born 1937), American businessman * Michel Host ...
fitness and
productivity Productivity is the efficiency of production of goods or services expressed by some measure. Measurements of productivity are often expressed as a ratio of an aggregate output to a single input or an aggregate input used in a production proces ...
in a variety of ways. Members of the root microbiome benefit from plant sugars or other carbon rich molecules. Individual members of the root microbiome may behave differently in association with different plant hosts, or may change the nature of their interaction (along the mutualist-parasite continuum) within a single host as environmental conditions or host health change. Despite the potential importance of the root microbiome for
plants Plants are predominantly Photosynthesis, photosynthetic eukaryotes of the Kingdom (biology), kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all curr ...
and
ecosystem An ecosystem (or ecological system) consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the syste ...
s, our understanding of how root microbial communities are assembled is in its infancy. This is in part because until recent advances in
sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...
technologies, root microbes were difficult to study due to high
species diversity Species diversity is the number of different species that are represented in a given community (a dataset). The effective number of species refers to the number of equally abundant species needed to obtain the same mean proportional species abundan ...
, the large number of
cryptic species In biology, a species complex is a group of closely related organisms that are so similar in appearance and other features that the boundaries between them are often unclear. The taxa in the complex may be able to hybridize readily with each oth ...
, and the fact that most species have yet to be retrieved in
culture Culture () is an umbrella term which encompasses the social behavior, institutions, and norms found in human societies, as well as the knowledge, beliefs, arts, laws, customs, capabilities, and habits of the individuals in these groups.Tyl ...
. Evidence suggests both biotic (such as host identity and plant neighbor) and
abiotic In biology and ecology, abiotic components or abiotic factors are non-living chemical and physical parts of the environment that affect living organisms and the functioning of ecosystems. Abiotic factors and the phenomena associated with them under ...
(such as
soil structure Soil structure describes the arrangement or the way of soil in the solid parts of the soil and of the pore space located between them. It is determined by how individual soil granules clump, bind together, and aggregate, resulting in the arrangem ...
and nutrient availability) factors affect community composition.


Function


Types of symbioses

Root associated microbes include
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
,
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
, and
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
. In addition, other organisms such as
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...
es,
algae Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular mic ...
,
protozoa Protozoa (singular: protozoan or protozoon; alternative plural: protozoans) are a group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris. Histo ...
,
nematode The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant-Parasitism, parasitic nematodes also known as eelworms. They are a diverse animal phylum inhab ...
s and
arthropod Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a Segmentation (biology), segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and Arth ...
s are part of root microbiota. Symbionts associated with plant roots subsist off of
photosynthetic Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in c ...
products (carbon rich molecules) from the plant host and can exist anywhere on the mutualist/parasite continuum. Root symbionts may improve their host's access to
nutrients A nutrient is a substance used by an organism to survive, grow, and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi, and protists. Nutrients can be incorporated into cells for metabolic purposes or excret ...
, produce plant-growth regulators, improve
environmental stress Stress, either physiological, biological or psychological, is an organism's response to a stressor such as an environmental condition. Stress is the body's method of reacting to a condition such as a threat, challenge or physical and psych ...
tolerance of their host, induce host defenses and systemic resistance against pests or pathogens, or be
pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ ...
ic. Parasites consume carbon from the plant without providing any benefit, or providing too little benefit relative to what they cost in carbon, thereby compromising host fitness. Symbionts may be biotrophic (subsisting off of living tissue) or necrotrophic (subsisting off of dead tissue).


Mutualist-parasite continuum

While some microbes may be purely mutualistic or
parasitic Parasitism is a close relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The entomologist E. O. Wilson has c ...
, many may behave one way or the other depending on the host species with which it is associated, environmental conditions, and host health. A host’s immune response controls symbiont infection and growth rates. If a host’s immune response is not able to control a particular microbial species, or if host immunity is compromised, the microbe-plant relationship will likely reside somewhere nearer the parasitic side of the mutualist-parasite continuum. Similarly, high nutrients can push some microbes into parasitic behavior, encouraging unchecked growth at a time when symbionts are no longer needed to aid with nutrient acquisition.


Composition

Roots are colonized by
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
,
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
and
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
. Because they are
multicellular A multicellular organism is an organism that consists of more than one cell, in contrast to unicellular organism. All species of animals, land plants and most fungi are multicellular, as are many algae, whereas a few organisms are partially uni- ...
, fungi can extend
hypha A hypha (; ) is a long, branching, filamentous structure of a fungus, oomycete, or actinobacterium. In most fungi, hyphae are the main mode of vegetative growth, and are collectively called a mycelium. Structure A hypha consists of one or ...
e from nutrient exchange organs within host cells into the surrounding rhizosphere and bulk soil. Fungi that extend beyond the root surface and engage in nutrient-carbon exchange with the plant host are commonly considered to be
mycorrhizal   A mycorrhiza (from Greek μύκης ', "fungus", and ῥίζα ', "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas) is a symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plan ...
, but external hyphae can also include other
endophytic An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date; h ...
fungi. Mycorrhizal fungi can extend a great distance into bulk soil, thereby increasing the root system’s reach and surface area, enabling mycorrhizal fungi to acquire a large percentage of its host plant’s nutrients. In some ecosystems, up to 80% of plant nitrogen and 90% of plant phosphorus is acquired by
mycorrhizal fungi   A mycorrhiza (from Greek μύκης ', "fungus", and ῥίζα ', "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas) is a symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plant ...
. In return, plants may allocate ~20-40% of their carbon to mycorrhizae.


Fungi


Mycorrhizae

Mycorrhizal (from greek) literally means “fungus roots” and defines symbiotic interaction between plants and fungus. Fungi are important to decompose and recycle organic material, however the boundaries between pathogenic and symbiotic lifestyles of fungi are not always clear-cut. Most of the time the association is symbiotic with fungus improving acquisition of nutrients and water from soil or increasing stress tolerance and fungus benefiting from carbohydrates produced by plant. Mycorrhizae include a broad variety of root-fungi interactions characterized by mode of colonization. Essentially all plants form mycorrhizal associations, and there is evidence that some mycorrhizae transport carbon and other nutrients not just from soil to plant, but also between different plants in a landscape. The main groups include
ectomycorrhiza An ectomycorrhiza (from Greek ἐκτός ', "outside", μύκης ', "fungus", and ῥίζα ', "root"; pl. ectomycorrhizas or ectomycorrhizae, abbreviated EcM) is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobi ...
e, arbuscular mycorhizae,
ericoid mycorrhiza The ericoid mycorrhiza is a mutualistic relationship formed between members of the plant family Ericaceae and several lineages of mycorrhizal fungi. This symbiosis represents an important adaptation to acidic and nutrient poor soils that specie ...
e,
orchid mycorrhiza Orchid mycorrhizae are endomycorrhizal fungi which develop symbiotic relationships with the roots and seeds of plants of the family Orchidaceae. Nearly all orchids are myco-heterotrophic at some point in their Biological life cycle, life cycle. Orch ...
e, and monotropoid mycorrhizae. Monotropoid mycorrhizae are associated with plants in the
monotropaceae Monotropoideae, sometimes referred to as monotropes, are a flowering plant subfamily in the family Ericaceae. Members of this subfamily are notable for their mycoheterotrophic and non-photosynthesizing or achlorophyllous characteristics. Descript ...
, which lack
chlorophyll Chlorophyll (also chlorophyl) is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words , ("pale green") and , ("leaf"). Chlorophyll allow plants to a ...
. Many
Orchids Orchids are plants that belong to the family Orchidaceae (), a diverse and widespread group of flowering plants with blooms that are often colourful and fragrant. Along with the Asteraceae, they are one of the two largest families of flowering ...
are also achlorophyllous for at least part of their life cycle. Thus these mycorrhizal-plant relationships are unique because the fungus provides the host with carbon as well as other nutrients, often by parasitizing other plants. Achlorophyllous plants forming these types of mycorrhizal associations are called mycoheterotrophs.


Endophytes

Endophytes grow inside the plant tissues - roots, stems, leaves - mostly symptomless, however when plant ages they can become slightly pathogenic. They may colonize inter-cellular spaces, the root cells themselves, or both.
Rhizobia Rhizobia are diazotrophic bacteria that fix nitrogen after becoming established inside the root nodules of legumes (Fabaceae). To express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen. In gene ...
and dark septate endophytes (which produce
melanin Melanin (; from el, μέλας, melas, black, dark) is a broad term for a group of natural pigments found in most organisms. Eumelanin is produced through a multistage chemical process known as melanogenesis, where the oxidation of the amino ...
, an
antioxidant Antioxidants are compounds that inhibit oxidation, a chemical reaction that can produce free radicals. This can lead to polymerization and other chain reactions. They are frequently added to industrial products, such as fuels and lubricant ...
that may provide resilience against a variety of environmental stresses) are famous examples.


Bacteria

Zone of soil surrounding the roots is rich in nutrients released by plants and is therefore attractive growth medium for both beneficial and pathogenic bacteria. Root associated beneficial bacteria promote plant growth and provide protection from pathogens. They are mostly
rhizobacteria Rhizobacteria are root-associated bacteria that can have a detrimental (parasitic varieties), neutral or beneficial effect on plant growth. The name comes from the Greek ''rhiza'', meaning root. The term usually refers to bacteria that form symbio ...
that belong to ''
Pseudomonadota Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The ...
'' and ''
Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...
'', with many examples from ''
Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able ...
'' and ''
Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum ''Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacilli ...
'' genera.
Rhizobium ''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants. The bacteria colonize plant cells ...
species colonize legume roots forming nodule structures. In response to root exudates, rhizobia produce Nod signalling factors that are recognized by legumes and induce formation of nodules on plant roots. Within these structures Rhizobium perform nitrogen fixation that proves plant with nitrogen source. In turn, plants provide bacteria with carbon source to energize the nitrogen fixation. In addition to nitrogen fixation, ''
Azospirillum ''Azospirillum'' is a Gram-negative, microaerophilic, non- fermentative and nitrogen-fixing bacterial genus from the family of Rhodospirillaceae. ''Azospirillum'' bacteria can promote plant growth. Characteristics The genus ''Azospirillum'' ...
'' species promote plant growth through production of growth
phytohormones Plant hormone (or phytohormones) are signal molecules, produced within plants, that occur in extremely low concentrations. Plant hormones control all aspects of plant growth and development, from embryogenesis, the regulation of organ size, pa ...
(
auxin Auxins (plural of auxin ) are a class of plant hormones (or plant-growth regulators) with some morphogen-like characteristics. Auxins play a cardinal role in coordination of many growth and behavioral processes in plant life cycles and are essenti ...
s,
cytokinin Cytokinins (CK) are a class of plant hormones that promote cell division, or cytokinesis, in plant roots and shoots. They are involved primarily in cell growth and differentiation, but also affect apical dominance, axillary bud growth, and lea ...
s,
gibberellin Gibberellins (GAs) are plant hormones that regulate various developmental processes, including stem elongation, germination, dormancy, flowering, flower development, and leaf and fruit senescence. GAs are one of the longest-known classes of p ...
s). Due to these phytohormones root hairs expand to occupy larger area and better acquire water and nutrients. Pathogenic bacteria that infect plants infect plant roots are most commonly from '' Pectobacterium'', ''
Ralstonia ''Ralstonia'' is a genus of bacteria, previously included in the genus ''Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members ...
'', ''
Dickeya ''Dickeya'' is a genus of the family Pectobacteriaceae that consists mainly of pathogens from herbaceous plants. Dickeya is the result of the reclassification of 75 strains of ''Pectobacterium chrysanthemi'', as well as ''Brenneria paradisiaca'' ...
'' and ''
Agrobacterium ''Agrobacterium'' is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. '' Agrobacterium tumefaciens'' is the most commonly studied species in this genus. ''Agrobacterium'' i ...
'' genera. Among the most notorious are ''
Pectobacterium carotovorum ''Pectobacterium carotovorum'' is a bacterium of the family Pectobacteriaceae; it used to be a member of the genus ''Erwinia''. The species is a plant pathogen with a diverse host range, including many agriculturally and scientifically importa ...
'', '' Pectobacterium atrosepticum'', ''
Ralstonia solanacearum ''Ralstonia solanacearum'' is an aerobic non-spore-forming, Gram-negative, plant pathogenic bacterium. ''R. solanacearum'' is soil-borne and motile with a polar flagellar tuft. It colonises the xylem, causing bacterial wilt in a very wide rang ...
'', '' Dickeya dadanthi'', ''
Dickeya solani ''Dickeya solani'' is a bacterium that causes blackleg and soft rot in potato crops. Its symptoms are often indistinguishable from those caused by '' Pectobacterium'' but is more virulent, causing disease from lower levels of inoculum and spread ...
'' and ''
Agrobacterium tumefaciens ''Agrobacterium radiobacter'' (more commonly known as ''Agrobacterium tumefaciens'') is the causal agent of crown gall disease (the formation of tumours) in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Sympto ...
''. Bacteria attach to roots in a certain biphasic mechanism with two steps – first weak, non-specific binding and then switch to second – strong irreversible residence phase. Both beneficial and pathogenic bacteria attach in this fashion. Bacteria can stay attached to the outer surface or, certain endophytes or pathogens can colonize the inner root. Primary attachment is governed by chemical forces or certain extracellular structures such as pili or
flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f ...
. Secondary attachment is mainly characterized by synthesis of
cellulose Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose is an important structural component of the primary cell wall ...
, extracellular fibrils and specific attachment factors such as surface proteins that help bacteria aggregate and form colonies.


Archaea

Though archaea are traditionally thought of as
extremophile An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme temper ...
s, microbes belonging to extreme environments, advances in
metagenomics Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...
and gene sequencing reveal that archaea are ubiquitous, found in nearly any environment including the root microbiome. For example, root-colonizing archaea have been discovered in
maize Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn (North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. Th ...
,
rice Rice is the seed of the grass species ''Oryza sativa'' (Asian rice) or less commonly ''Oryza glaberrima ''Oryza glaberrima'', commonly known as African rice, is one of the two domesticated rice species. It was first domesticated and grown i ...
,
wheat Wheat is a grass widely cultivated for its seed, a cereal grain that is a worldwide staple food. The many species of wheat together make up the genus ''Triticum'' ; the most widely grown is common wheat (''T. aestivum''). The archaeologi ...
, and
mangrove A mangrove is a shrub or tree that grows in coastal saline water, saline or brackish water. The term is also used for tropical coastal vegetation consisting of such species. Mangroves are taxonomically diverse, as a result of convergent evoluti ...
s.
Methanogen Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are com ...
and ammonium-oxidizing archaea are prevalent members of the root microbiome, especially in
anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: * Anaerobic adhesive, a bonding a ...
soils and wetlands. Archaeal phyla found in the root microbiome include
Euryarchaeota Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extre ...
,
Nitrososphaerota The Nitrososphaerota (syn. Thaumarchaeota) are a phylum of the Archaea proposed in 2008 after the genome of ''Cenarchaeum symbiosum'' was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoprote ...
(formerly Thaumarchaeota), and
Thermoproteota The Thermoproteota (also known as crenarchaea) are archaea that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteris ...
(formerly Crenarchaeota). The presence and relative abundance of archaea in various environments suggest that they likely play an important role in the root microbiome. Archaea have been found to promote plant growth and development, provide stress tolerance, improve nutrient uptake and protect against pathogens. For example, ''
Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter a ...
'' colonized with an ammonia-oxidizing soil archaea, '' Nitrosocosmicus oleophilius,'' exhibited increased shoot weight, photosynthetic activity and immune response. Examination of microbial communities in soil and roots identify archaeal organisms and genes that occupy functions similar to that of to
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
and
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
, such as
auxin Auxins (plural of auxin ) are a class of plant hormones (or plant-growth regulators) with some morphogen-like characteristics. Auxins play a cardinal role in coordination of many growth and behavioral processes in plant life cycles and are essenti ...
synthesis, protection against
abiotic stress Abiotic stress is the negative impact of non-living factors on the living organisms in a specific environment. The non-living variable must influence the environment beyond its normal range of variation to adversely affect the population performan ...
and
nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...
. In some cases, key genes for plant growth and development, such as
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cell ...
and
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mech ...
synthesis, are more prevalent in archaea than bacteria. Archaeal presence in the root microbiome can also be affected by plant hosts, which can change the diversity, presence and health of archaeal communities.


Viruses

Viruses also infect plants via the roots, however to penetrate the root tissues they typically use vectors such as nematodes or fungi.


Assembly mechanisms

There is an ongoing debate regarding what mechanisms are responsible for assembling individual microbes into
communities A community is a Level of analysis, social unit (a group of living things) with commonality such as place (geography), place, Norm (social), norms, religion, values, Convention (norm), customs, or Identity (social science), identity. Communiti ...
. There are two primary competing hypotheses. One is that "everything is everywhere, but the environment selects," meaning biotic and
abiotic In biology and ecology, abiotic components or abiotic factors are non-living chemical and physical parts of the environment that affect living organisms and the functioning of ecosystems. Abiotic factors and the phenomena associated with them under ...
factors pose the only constraints, through
natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charle ...
, to which microbes colonize what
environments Environment most often refers to: __NOTOC__ * Natural environment, all living and non-living things occurring naturally * Biophysical environment, the physical and biological factors along with their chemical interactions that affect an organism or ...
. This is called the
niche Niche may refer to: Science *Developmental niche, a concept for understanding the cultural context of child development *Ecological niche, a term describing the relational position of an organism's species *Niche differentiation, in ecology, the ...
hypothesis, and its counterpart is the hypothesis that neutral processes, such as distance and geographic barriers to dispersal, control microbial community assembly when
taxa In biology, a taxon (back-formation from ''taxonomy''; plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular nam ...
are equally fit within an environment. In this hypothesis, differences between individual taxa in modes and reach of dispersal explain the differences in microbial communities of different environments. Most likely, both natural selection and neutral processes affect microbial community assembly, though certain microbial taxa may be more restricted by one process or the other depending on their physiological restrictions and mode of dispersion. Microbial dispersal mechanisms include wind, water, and hitchhiking on more mobile macrobes. Microbial dispersion is difficult to study, and little is known about its effect on microbial community assembly relative to the effect of abiotic and biotic assembly mechanisms, particularly in roots. For this reason only assembly mechanisms that fit within the niche hypothesis are discussed below. The taxa within root microbial communities seem to be drawn from the surrounding soil, though the relative abundance of various taxa may differ greatly from those found in bulk soil due to unique niches in the root and rhizosphere.


Biotic assembly mechanisms

Different parts of the root are associated with different microbial communities. For example, fine roots, root tips, and the main root are all associated with different communities, and the rhizosphere, root surface, and root tissue are all associated with different communities, likely due to the unique chemistry and nutrient status of each of these regions. Additionally different plant species, and even different cultivars, harbor different microbial communities, probably due to host specific immune responses and differences in carbon root exudates. Host age affects root microbial community composition, likely for similar reasons as host identity. The identity of neighboring vegetation has also been shown to impact a host plant's root microbial community composition.


Abiotic assembly mechanisms

Abiotic mechanisms also affect root microbial community assembly because individual taxa have different optima along various
environmental gradient An environmental gradient, or climate gradient, is a change in abiotic (non-living) factors through space (or time). Environmental gradients can be related to factors such as altitude, depth, temperature, soil humidity and precipitation. Often time ...
s, such as nutrient concentrations, pH, moisture, temperature, etc. In addition to chemical and climatic factors, soil structure and disturbance impact root biotic assembly.


Succession

The root microbiome is dynamic, fluid within the constraints imposed by the biotic and abiotic environment. As in macroecological systems, the historical trajectory of the microbiotic community may partially determine the present and future community. Due to antagonistic and mutualistic interactions between microbial taxa, the taxa colonizing a root at any given moment could be expected to influence which new taxa are acquired, and therefore how the community responds to changes in the host or environment. While the effect of initial community on microbial succession has been studied in various environmental samples,
human microbiome The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, seminal fluid, uterus, ovarian ...
, and laboratory settings, it has yet to be studied in roots.


See also

* Mangrove root microbiome


References

{{microorganisms Soil biology Microbiology Microbiomes