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</style><table class="sidebar sidebar-collapse nomobile nowraplinks"><tbody><tr><td class="sidebar-pretitle">Part of a series on</td></tr><tr><th class="sidebar-title-with-pretitle" style="background:#82C3D8; padding:0.2em; font-size:160%; font-weight:bold;"><a href="Microbiome" title="Microbiome">Microbiomes</a></th></tr><tr><td class="sidebar-image"><span typeof="mw:File"></span></td></tr><tr><td class="sidebar-content">
<div class="sidebar-list mw-collapsible"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)"><a href="Plant_microbiome" title="Plant microbiome">Plant microbiomes</a></div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Endosphere" title="Endosphere">Endosphere</a></li>
<li><a href="Phyllosphere" title="Phyllosphere">Phyllosphere</a></li></ul>
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<ul><li><a href="Rhizosphere" title="Rhizosphere">Rhizosphere</a>
<ul><li><a href="Laimosphere" title="Laimosphere">laimosphere</a></li>
<li><a href="Soil_microbiology" title="Soil microbiology">soil microbiome</a></li>
<li><a href="Spermosphere" title="Spermosphere">spermosphere</a></li></ul></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)"><a href="Marine_microbiome" title="Marine microbiome">Marine microbiomes</a></div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Cetacean_microbiome" title="Cetacean microbiome">Cetacean</a></li>
<li><a href="Coral_microbiome" class="mw-redirect" title="Coral microbiome">Coral</a></li>
<li><a href="Phytoplankton_microbiome" title="Phytoplankton microbiome">Phytoplankton</a></li>
<li><a href="Seagrass_microbiome" class="mw-redirect" title="Seagrass microbiome">Seagrass</a></li>
<li><a href="Sponge_microbiomes" title="Sponge microbiomes">Sponge</a></li>
<li><a href="Marine_microbial_symbiosis" title="Marine microbial symbiosis">Marine microbial symbiosis</a></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)"><a href="Human_microbiome" title="Human microbiome">Human microbiomes</a></div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Human_milk_microbiome" title="Human milk microbiome">Human milk</a></li>
<li><a href="Fecal_microbiota_transplant" title="Fecal microbiota transplant">Fecal transplant</a></li></ul>
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<ul><li><a href="Gut%E2%80%93brain_axis" title="Gut–brain axis">Gut–brain axis</a></li>
<li><a href="Placental_microbiome" title="Placental microbiome">Placental</a></li>
<li><a href="Salivary_microbiome" title="Salivary microbiome">Salivary</a><br></li>
<li><a href="Uterine_microbiome" title="Uterine microbiome">Uterine</a></li>
<li><a href="Necrobiome" title="Necrobiome">Necrobiome</a></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)">Other microbiomes</div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Mycobiome" title="Mycobiome">Mycobiome</a></li>
<li><a href="Phycosphere" title="Phycosphere">Phycosphere</a><br></li>
<li><a href="Microbiomes_of_the_built_environment" title="Microbiomes of the built environment">Built environment</a></li>
<li><a href="Microbiome_in_the_Drosophila_gut" title="Microbiome in the Drosophila gut"><i>Drosophila</i> gut</a></li>
<li><a href="Poultry_microbiome" title="Poultry microbiome">Poultry</a></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)"><a href="Microbiota" title="Microbiota">Microbiota</a></div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Plant_microbiota" class="mw-redirect" title="Plant microbiota">Plant</a>
<ul><li><a href="Endophyte" title="Endophyte">endophyte</a></li>
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<li><a href="Rhizobacteria" title="Rhizobacteria">rhizobacteria</a></li></ul></li></ul>
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<ul><li><a href="Gut_microbiota" title="Gut microbiota">gut</a></li>
<li><a href="Lung_microbiota" title="Lung microbiota">lung</a></li>
<li><a href="Oral_microbiology" title="Oral microbiology">oral</a></li>
<li><a href="Skin_flora" title="Skin flora">skin</a></li>
<li><a href="Vaginal_flora" title="Vaginal flora">vaginal</a></li></ul></li></ul>
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<ul><li><a href="Marine_microorganisms" title="Marine microorganisms">Marine</a></li>
<li><a href="Microbial_consortium" title="Microbial consortium">Microbial community</a></li>
<li><a href="Initial_acquisition_of_microbiota" title="Initial acquisition of microbiota">Initial acquisition</a></li>
<li><a href="Microbiota-accessible_carbohydrates" title="Microbiota-accessible carbohydrates">Accessible carbohydrates</a></li>
<li><a href="Flora_(microbiology)" title="Flora (microbiology)">Flora (microbiology)</a></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)"><a href="Holobiont" title="Holobiont">Holobionts</a></div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Plant_holobiont" title="Plant holobiont">Plant holobiont</a></li>
<li><a href="Marine_holobiont" title="Marine holobiont">Marine holobiont</a></li></ul>
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<ul><li><ul><li><a href="Coral_holobiont" class="mw-redirect" title="Coral holobiont">coral</a></li>
<li><a href="Crab_holobiont" class="mw-redirect" title="Crab holobiont">crab</a></li>
<li><a href="Seagrass_holobiont" class="mw-redirect" title="Seagrass holobiont">seagrass</a></li>
<li><a href="Sponge_holobiont" class="mw-redirect" title="Sponge holobiont">sponge</a></li>
<li><a href="Rhodolith_holobiont" class="mw-redirect" title="Rhodolith holobiont">rhodolith</a></li></ul></li></ul>
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<div class="hlist">
<ul><li><a href="Hologenomics" title="Hologenomics">Hologenomics</a>
<ul><li><a href="Hologenome_theory_of_evolution" title="Hologenome theory of evolution">hologenome evolution</a></li></ul></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)"><a href="Virome" title="Virome">Viromes</a></div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Bat_virome" title="Bat virome">Bat</a></li>
<li><a href="Human_virome" title="Human virome">Human</a></li>
<li><a href="Mangrove#Mangrove_virome" title="Mangrove">Mangrove</a><br></li>
<li><a href="Viriome" title="Viriome">Viriome</a></li>
<li><a href="Virosphere" title="Virosphere">Virosphere</a></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)">Related</div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Biomass_partitioning" title="Biomass partitioning">Biomass partitioning</a></li>
<li><a href="Dysbiosis" title="Dysbiosis">Dysbiosis</a></li></ul>
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<div class="hlist">
<ul><li><a href="Gnotobiosis" title="Gnotobiosis">Gnotobiosis</a></li>
<li><a href="Phytobiome" title="Phytobiome">Phytobiome</a></li>
<li><a href="Quorum_sensing" title="Quorum sensing">Quorum sensing</a></li>
<li><a href="Biological_dark_matter" title="Biological dark matter">Biological dark matter</a></li>
<li><a href="Microbial_population_biology" title="Microbial population biology">Microbial population biology</a></li>
<li><a href="Microbial_cooperation" title="Microbial cooperation">Microbial cooperation</a></li>
<li><a href="Metagenomics" title="Metagenomics">Metagenomics</a>
<ul><li><a href="Viral_metagenomics" title="Viral metagenomics">viral</a></li></ul></li>
<li><a href="Metatranscriptomics" title="Metatranscriptomics">Metatranscriptomics</a></li>
<li><a href="Metabolomics" title="Metabolomics">Metabolomics</a></li>
<li><a href="Pan-genome" title="Pan-genome">Pan-genome</a></li>
<li><a href="Superorganism" title="Superorganism">Superorganism</a></li>
<li><a href="Symbiogenesis" title="Symbiogenesis">Symbiogenesis</a></li></ul>
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<div class="sidebar-list mw-collapsible mw-collapsed"><div class="sidebar-list-title" style="text-align:center;font-size:100%;font-weight:bold;;color: var(--color-base)">Projects</div><div class="sidebar-list-content mw-collapsible-content"><div class="hlist">
<ul><li><a href="Human_Microbiome_Project" title="Human Microbiome Project">Human Microbiome Project</a></li>
<li>Earth Microbiome Project</li></ul>
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<p>The <b>root microbiome</b> (also called rhizosphere microbiome) is the dynamic <a href="Community_(ecology)" title="Community (ecology)">community</a> of <a href="Microorganisms" class="mw-redirect" title="Microorganisms">microorganisms</a> associated with plant <a href="Root" title="Root">roots</a>.<sup id="cite_ref-Mendes-2013_1-0" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including <a href="Bacteria" title="Bacteria">bacteria</a>, <a href="Fungus" title="Fungus">fungi</a>, and <a href="Archaea" title="Archaea">archaea</a>. The microbial communities inside the root and in the <a href="Rhizosphere" title="Rhizosphere">rhizosphere</a> are distinct from each other,<sup id="cite_ref-Gottel-2011_2-0" class="reference"><a href="#cite_note-Gottel-2011-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> and from the microbial communities of bulk <a href="Soil" title="Soil">soil</a>,<sup id="cite_ref-Nguyen-2009_3-0" class="reference"><a href="#cite_note-Nguyen-2009-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> although there is some overlap in <a href="Species" title="Species">species</a> composition.
</p><p>Different microorganisms, both beneficial and harmful, affect the development and physiology of plants. Beneficial microorganisms include bacteria that fix nitrogen, various microbes that promote plant growth, mycorrhizal fungi, mycoparasitic fungi, protozoa, and certain biocontrol microorganisms.<sup id="cite_ref-Mendes-2013_1-1" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> Pathogenic microorganisms can also include certain bacteria, fungi, and nematodes that can colonize the rhizosphere. Pathogens are able to compete with protective microbes and break through innate plant defense mechanisms.<sup id="cite_ref-Mendes-2013_1-2" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> Some pathogenic bacteria that can be carried over to humans, such as <i><a href="Salmonella" title="Salmonella">Salmonella</a></i>, <a href="Enterohaemorrhagic_Escherichia_coli" class="mw-redirect" title="Enterohaemorrhagic Escherichia coli">enterohaemorhagic <i>Escherichia coli</i></a>, <i><a href="Burkholderia_cenocepacia" title="Burkholderia cenocepacia">Burkholderia cenocepacia</a></i>, <i><a href="Pseudomonas_aeruginosa" title="Pseudomonas aeruginosa">Pseudomonas aeruginosa</a></i>, and <i><a href="Stenotrophomonas_maltophilia" title="Stenotrophomonas maltophilia">Stenotrophomonas maltophilia</a></i>, can also be detected in root microbiomes and other plant tissues.<sup id="cite_ref-Mendes-2013_1-3" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>
</p><p>Root microbiota affect plant <a href="Host_(biology)" title="Host (biology)">host</a> <a href="Fitness_(biology)" title="Fitness (biology)">fitness</a> and <a href="Productivity_(ecology)" title="Productivity (ecology)">productivity</a> 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,<sup id="cite_ref-Kogel-2006_4-0" class="reference"><a href="#cite_note-Kogel-2006-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> or may change the nature of their interaction (along the <a href="Symbiosis" title="Symbiosis">mutualist-parasite continuum</a>) within a single host as environmental conditions or host health change.<sup id="cite_ref-Smith-2010_5-0" class="reference"><a href="#cite_note-Smith-2010-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup>
</p><p>Despite the potential importance of the root microbiome for <a href="Plants" class="mw-redirect" title="Plants">plants</a> and <a href="Ecosystem" title="Ecosystem">ecosystems</a>, our understanding of how root microbial communities are assembled is in its infancy.<sup id="cite_ref-6" class="reference"><a href="#cite_note-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Nemergut-2013_7-0" class="reference"><a href="#cite_note-Nemergut-2013-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> This is in part because, until recent advances in <a href="DNA_sequencing" title="DNA sequencing">sequencing</a> technologies, root microbes were difficult to study due to high <a href="Species_diversity" title="Species diversity">species diversity</a>, the large number of <a href="Cryptic_species_complex" class="mw-redirect" title="Cryptic species complex">cryptic species</a>, and the fact that most species have yet to be retrieved in <a href="Microbiological_culture" title="Microbiological culture">culture</a>.<sup id="cite_ref-Buée-2009_8-0" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> Evidence suggests both <a href="Biotic_component" class="mw-redirect" title="Biotic component">biotic</a> (such as host identity and plant neighbor) and <a href="Abiotic_component" title="Abiotic component">abiotic</a> (such as <a href="Soil_structure" title="Soil structure">soil structure</a> and nutrient availability) factors affect community composition.<sup id="cite_ref-Dean-2014_9-0" class="reference"><a href="#cite_note-Dean-2014-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Dean-2014-2_10-0" class="reference"><a href="#cite_note-Dean-2014-2-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Hardoim-2011_11-0" class="reference"><a href="#cite_note-Hardoim-2011-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Egerton-Warburton-2007_12-0" class="reference"><a href="#cite_note-Egerton-Warburton-2007-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Tedersoo-2012_13-0" class="reference"><a href="#cite_note-Tedersoo-2012-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup>
</p>
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<div class="mw-heading mw-heading2"><h2 id="Function">Function</h2></div>
<div class="mw-heading mw-heading3"><h3 id="Types_of_symbioses">Types of symbioses</h3></div>
<p>Root associated microbes include <a href="Fungus" title="Fungus">fungi</a>, <a href="Bacteria" title="Bacteria">bacteria</a>, and <a href="Archaea" title="Archaea">archaea</a>. In addition, other organisms such as <a href="Virus" title="Virus">viruses</a>, <a href="Algae" title="Algae">algae</a>, <a href="Protozoa" title="Protozoa">protozoa</a>, <a href="Nematode" title="Nematode">nematodes</a>, and <a href="Arthropod" title="Arthropod">arthropods</a> are part of root microbiota.<sup id="cite_ref-Mendes-2013_1-4" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> <a href="Symbiosis" title="Symbiosis">Symbionts</a> associated with plant roots subsist off of <a href="Photosynthesis" title="Photosynthesis">photosynthetic</a> products (carbon rich molecules) from the plant host and can exist anywhere on the <a href="Symbiosis" title="Symbiosis">mutualist/parasite</a> continuum.
</p><p>Root symbionts may improve their host's access to <a href="Plant_nutrition#Functions_of_nutrients" title="Plant nutrition">nutrients</a>,<sup id="cite_ref-van_der_Heijden-2008_14-0" class="reference"><a href="#cite_note-van_der_Heijden-2008-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> produce <a href="Plant_hormone" title="Plant hormone">plant-growth regulators</a>,<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> improve <a href="Abiotic_stress" title="Abiotic stress">environmental stress</a> tolerance of their host,<sup id="cite_ref-18" class="reference"><a href="#cite_note-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-19" class="reference"><a href="#cite_note-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-20" class="reference"><a href="#cite_note-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> induce host <a href="Plant_use_of_endophytic_fungi_in_defense" title="Plant use of endophytic fungi in defense">defenses</a> and <a href="Systemic_acquired_resistance" title="Systemic acquired resistance">systemic resistance</a> against pests or pathogens,<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-22" class="reference"><a href="#cite_note-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> or be <a href="Pathogen" title="Pathogen">pathogenic</a>.<sup id="cite_ref-24" class="reference"><a href="#cite_note-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup> Parasites consume carbon from the plant without providing any benefit or providing insufficient benefit relative to their carbon consumption, thereby compromising host fitness. Symbionts may be biotrophic (subsisting off of living tissue) or necrotrophic (subsisting off of dead tissue).
</p>
<div class="mw-heading mw-heading3"><h3 id="Mutualist-parasite_continuum">Mutualist-parasite continuum</h3></div>
<p>While some microbes may be purely <a href="Mutualism_(biology)" title="Mutualism (biology)">mutualistic</a> or <a href="Parasite" class="mw-redirect" title="Parasite">parasitic</a>, many may behave differently depending on the host species with which it is associated, environmental conditions, and host health.<sup id="cite_ref-Kogel-2006_4-1" class="reference"><a href="#cite_note-Kogel-2006-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> A host's immune response controls symbiont infection and growth rates.<sup id="cite_ref-Kogel-2006_4-2" class="reference"><a href="#cite_note-Kogel-2006-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Kogel-2006_4-3" class="reference"><a href="#cite_note-Kogel-2006-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading2"><h2 id="Composition">Composition</h2></div>
<p>Roots are colonized by <a href="Fungus" title="Fungus">fungi</a>, <a href="Bacteria" title="Bacteria">bacteria</a>, and <a href="Archaea" title="Archaea">archaea</a>. Because they are <a href="Multicellular_organism" title="Multicellular organism">multicellular</a>, fungi can extend <a href="Hypha" title="Hypha">hyphae</a> 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 <a href="Mycorrhizal_fungi" class="mw-redirect" title="Mycorrhizal fungi">mycorrhizal</a>, but external hyphae can also include other <a href="Endophyte" title="Endophyte">endophytic</a> fungi. Mycorrhizal fungi can extend a great distance into bulk soil,<sup id="cite_ref-Smith-2010_5-1" class="reference"><a href="#cite_note-Smith-2010-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> 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 <a href="Mycorrhiza" title="Mycorrhiza">mycorrhizal fungi</a>.<sup id="cite_ref-van_der_Heijden-2008_14-1" class="reference"><a href="#cite_note-van_der_Heijden-2008-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> In return, plants may allocate ~20–40% of their carbon to mycorrhizae.<sup id="cite_ref-25" class="reference"><a href="#cite_note-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading3"><h3 id="Fungi">Fungi</h3></div>
<div class="mw-heading mw-heading4"><h4 id="Mycorrhizae">Mycorrhizae</h4></div>
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</style><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="Mycorrhiza" title="Mycorrhiza">Mycorrhiza</a></div>
<p>Mycorrhizal (from Greek) literally means "fungus roots" and defines symbiotic interaction between plants and fungi. Fungi are important for decomposing and recycling organic material. However, the boundaries between the pathogenic and symbiotic lifestyles of fungi are not always clear-cut. Most of the time, the association is symbiotic, with the fungus improving nutrient and water acquisition or increasing stress tolerance for the plant and benefiting from the carbohydrates produced by the plant in return.<sup id="cite_ref-Zeilinger-2016_26-0" class="reference"><a href="#cite_note-Zeilinger-2016-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> Mycorrhizae include a wide variety of root-fungi interactions characterized by the mode of colonization. Essentially all plants form mycorrhizal associations, and there is evidence that some mycorrhizae transport carbon and other nutrients not only from soil to plant, but also between different plants in a landscape.<sup id="cite_ref-Smith-2010_5-2" class="reference"><a href="#cite_note-Smith-2010-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> The main groups include <a href="Ectomycorrhiza" title="Ectomycorrhiza">ectomycorrhizae</a>, <a href="Arbuscular_mycorrhiza" title="Arbuscular mycorrhiza">arbuscular mycorrhizae</a>, <a href="Ericoid_mycorrhiza" title="Ericoid mycorrhiza">ericoid mycorrhizae</a>, <a href="Orchid_mycorrhiza" title="Orchid mycorrhiza">orchid mycorrhizae</a>, and monotropoid mycorrhizae. Monotropoid mycorrhizae are associated with plants in the <a href="Monotropaceae" class="mw-redirect" title="Monotropaceae">monotropaceae</a>, which lack <a href="Chlorophyll" title="Chlorophyll">chlorophyll</a>. Many <a href="Orchidaceae" class="mw-redirect" title="Orchidaceae">Orchids</a> 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 and other nutrients, often by parasitizing other plants.<sup id="cite_ref-Smith-2010_5-3" class="reference"><a href="#cite_note-Smith-2010-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> Achlorophyllous plants forming these types of mycorrhizal associations are called <a href="Myco-heterotrophy" title="Myco-heterotrophy">mycoheterotrophs</a>.
</p>
<div class="mw-heading mw-heading4"><h4 id="Endophytes">Endophytes</h4></div>
<div role="note" class="hatnote navigation-not-searchable">Main article: <a href="Endophyte" title="Endophyte">Endophyte</a></div>
<p>Endophytes grow inside plant tissue—roots, stems, leaves—mostly symptomless. However, when plants age, they can become slightly pathogenic.<sup id="cite_ref-Zeilinger-2016_26-1" class="reference"><a href="#cite_note-Zeilinger-2016-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> They may colonize inter-cellular spaces, the root cells themselves, or both. <a href="Rhizobia" title="Rhizobia">Rhizobia</a> and <a href="Dark_septate_endophytes" class="mw-redirect" title="Dark septate endophytes">dark septate endophytes</a> (which produce <a href="Melanin" title="Melanin">melanin</a>, an <a href="Antioxidant" title="Antioxidant">antioxidant</a> that may provide resilience against a variety of environmental stresses<sup id="cite_ref-27" class="reference"><a href="#cite_note-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup>) are examples.
</p>
<div class="mw-heading mw-heading3"><h3 id="Bacteria">Bacteria</h3></div>
<p>The zone of soil surrounding the roots is rich in nutrients released by plants and is, therefore, an attractive growth medium for both beneficial and pathogenic bacteria. Root associated beneficial bacteria promote plant growth and provide protection from pathogens. They are mostly <a href="Rhizobacteria" title="Rhizobacteria">rhizobacteria</a> that belong to <i><a href="Pseudomonadota" title="Pseudomonadota">Pseudomonadota</a></i> and <i><a href="Bacillota" title="Bacillota">Bacillota</a></i>, with many examples from <i><a href="Pseudomonas" title="Pseudomonas">Pseudomonas</a></i> and <i><a href="Bacillus" title="Bacillus">Bacillus</a></i> genera.<sup id="cite_ref-Mendes-2013_1-5" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> <i><a href="Rhizobium" title="Rhizobium">Rhizobium</a></i> species colonize legume roots forming nodule structures. In response to root exudates, rhizobia produce <a href="Nod_factor" title="Nod factor">Nod signalling factors</a> that are recognized by legumes and induce the formation of nodules on plant roots.<sup id="cite_ref-28" class="reference"><a href="#cite_note-28"><span class="cite-bracket">[</span>28<span class="cite-bracket">]</span></a></sup> Within these structures, <i>Rhizobium</i> fix atmospheric nitrogen into ammonia that is then used by the plant. In turn, plants provide the bacteria with a carbon source to energize the nitrogen fixation.<sup id="cite_ref-Wheatley-2018_29-0" class="reference"><a href="#cite_note-Wheatley-2018-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-30" class="reference"><a href="#cite_note-30"><span class="cite-bracket">[</span>30<span class="cite-bracket">]</span></a></sup> In addition to nitrogen fixation, <i><a href="Azospirillum" title="Azospirillum">Azospirillum</a></i> species promote plant growth through the production of growth <a href="Plant_hormone" title="Plant hormone">phytohormones</a> (<a href="Auxin" title="Auxin">auxins</a>, <a href="Cytokinin" title="Cytokinin">cytokinins</a>, <a href="Gibberellin" title="Gibberellin">gibberellins</a>). Due to these phytohormones, root hairs expand to occupy a larger area and better acquire water and nutrients.<sup id="cite_ref-Wheatley-2018_29-1" class="reference"><a href="#cite_note-Wheatley-2018-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-31" class="reference"><a href="#cite_note-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> Pathogenic bacteria that infect plants infect plant roots are most commonly from <i><a href="Pectobacterium" title="Pectobacterium">Pectobacterium</a></i>, <i><a href="Ralstonia" title="Ralstonia">Ralstonia</a></i>, <i><a href="Dickeya" title="Dickeya">Dickeya</a></i> and <i><a href="Agrobacterium" title="Agrobacterium">Agrobacterium</a></i> genera. Among the most notorious are <i><a href="Pectobacterium_carotovorum" title="Pectobacterium carotovorum">Pectobacterium carotovorum</a></i>, <i><a href="Pectobacterium_atrosepticum" title="Pectobacterium atrosepticum">Pectobacterium atrosepticum</a></i>, <i><a href="Ralstonia_solanacearum" title="Ralstonia solanacearum">Ralstonia solanacearum</a></i>, <i><a href="Dickeya_dadantii" title="Dickeya dadantii">Dickeya dadanthi</a></i>, <i><a href="Dickeya_solani" title="Dickeya solani">Dickeya solani</a></i>, and <i><a href="Agrobacterium_tumefaciens" title="Agrobacterium tumefaciens">Agrobacterium tumefaciens</a></i>.
</p><p>Bacteria attach to roots in a biphasic mechanism with two steps—first weak, non-specific binding, then a strong irreversible residence phase. Both beneficial and pathogenic bacteria attach in this fashion. Bacteria can stay attached to the outer surface or colonize the inner root.<sup id="cite_ref-Wheatley-2018_29-2" class="reference"><a href="#cite_note-Wheatley-2018-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup> Primary attachment is governed by chemical forces or extracellular structures such as pili or <a href="Flagellum" title="Flagellum">flagella</a>. Secondary attachment is mainly characterized by the synthesis of <a href="Cellulose" title="Cellulose">cellulose</a>, extracellular fibrils, and specific attachment factors such as surface proteins that help bacteria aggregate and form colonies.<sup id="cite_ref-Wheatley-2018_29-3" class="reference"><a href="#cite_note-Wheatley-2018-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading3"><h3 id="Archaea">Archaea</h3></div>
<div role="note" class="hatnote navigation-not-searchable">Main article: <a href="Archaea" title="Archaea">Archaea</a></div>
<p>Though archaea are often thought of as <a href="Extremophile" title="Extremophile">extremophiles</a>, microbes belonging to extreme environments, advances in <a href="Metagenomics" title="Metagenomics">metagenomics</a> and <a href="DNA_sequencing" title="DNA sequencing">gene sequencing</a> have revealed that archaea are found in nearly any environment, including the root microbiome.<sup id="cite_ref-Buée-2009_8-1" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Moissl-Eichinger-2017_32-0" class="reference"><a href="#cite_note-Moissl-Eichinger-2017-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Chelius-2001_33-0" class="reference"><a href="#cite_note-Chelius-2001-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Prudence-2019_34-0" class="reference"><a href="#cite_note-Prudence-2019-34"><span class="cite-bracket">[</span>34<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-35" class="reference"><a href="#cite_note-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Taffner-2018_36-0" class="reference"><a href="#cite_note-Taffner-2018-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> For example, root-colonizing archaea have been discovered in <a href="Maize" title="Maize">maize</a>,<sup id="cite_ref-Chelius-2001_33-1" class="reference"><a href="#cite_note-Chelius-2001-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup> <a href="Rice" title="Rice">rice</a>,<sup id="cite_ref-37" class="reference"><a href="#cite_note-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> <a href="Wheat" title="Wheat">wheat</a>,<sup id="cite_ref-Prudence-2019_34-1" class="reference"><a href="#cite_note-Prudence-2019-34"><span class="cite-bracket">[</span>34<span class="cite-bracket">]</span></a></sup> and <a href="Mangrove" title="Mangrove">mangroves</a>.<sup id="cite_ref-Wang-2015_38-0" class="reference"><a href="#cite_note-Wang-2015-38"><span class="cite-bracket">[</span>38<span class="cite-bracket">]</span></a></sup> <a href="Methanogen" title="Methanogen">Methanogen</a> and ammonium-oxidizing archaea are prevalent members of the root microbiome, especially in <a href="Hypoxia_(environmental)" title="Hypoxia (environmental)">anaerobic</a> soils and wetlands.<sup id="cite_ref-Moissl-Eichinger-2017_32-1" class="reference"><a href="#cite_note-Moissl-Eichinger-2017-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-39" class="reference"><a href="#cite_note-39"><span class="cite-bracket">[</span>39<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Liu-2015_40-0" class="reference"><a href="#cite_note-Liu-2015-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-41" class="reference"><a href="#cite_note-41"><span class="cite-bracket">[</span>41<span class="cite-bracket">]</span></a></sup> Archaeal <a href="Phylum" title="Phylum">phyla</a> found in the root microbiome include <a href="Euryarchaeota" class="mw-redirect" title="Euryarchaeota">Euryarchaeota</a>,<sup id="cite_ref-Moissl-Eichinger-2017_32-2" class="reference"><a href="#cite_note-Moissl-Eichinger-2017-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Liu-2015_40-1" class="reference"><a href="#cite_note-Liu-2015-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Ke-2013_42-0" class="reference"><a href="#cite_note-Ke-2013-42"><span class="cite-bracket">[</span>42<span class="cite-bracket">]</span></a></sup> <a href="Nitrososphaerota" class="mw-redirect" title="Nitrososphaerota">Nitrososphaerota</a> (formerly Thaumarchaeota),<sup id="cite_ref-Moissl-Eichinger-2017_32-3" class="reference"><a href="#cite_note-Moissl-Eichinger-2017-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Ke-2013_42-1" class="reference"><a href="#cite_note-Ke-2013-42"><span class="cite-bracket">[</span>42<span class="cite-bracket">]</span></a></sup> and <a href="Thermoproteota" title="Thermoproteota">Thermoproteota</a> (formerly Crenarchaeota).<sup id="cite_ref-Liu-2015_40-2" class="reference"><a href="#cite_note-Liu-2015-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup>
</p><p>The presence and relative abundance of archaea in various environments suggest that they likely play an important role in the root microbiome.<sup id="cite_ref-Moissl-Eichinger-2017_32-4" class="reference"><a href="#cite_note-Moissl-Eichinger-2017-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup> Archaea have been found to promote plant growth and development, provide stress tolerance, improve nutrient uptake, and protect against pathogens.<sup id="cite_ref-Moissl-Eichinger-2017_32-5" class="reference"><a href="#cite_note-Moissl-Eichinger-2017-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Taffner-2018_36-1" class="reference"><a href="#cite_note-Taffner-2018-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Song-2019_43-0" class="reference"><a href="#cite_note-Song-2019-43"><span class="cite-bracket">[</span>43<span class="cite-bracket">]</span></a></sup> For example, <i><a href="Arabidopsis_thaliana" title="Arabidopsis thaliana">Arabidopsis thaliana</a></i> colonized with an ammonia-oxidizing soil archaea, <i>Nitrosocosmicus oleophilius,</i> exhibited increased shoot weight, photosynthetic activity, and immune response.<sup id="cite_ref-Song-2019_43-1" class="reference"><a href="#cite_note-Song-2019-43"><span class="cite-bracket">[</span>43<span class="cite-bracket">]</span></a></sup>
</p><p>Examination of microbial communities in soil and roots has identified archaeal organisms and genes with functions similar to that of <a href="Bacteria" title="Bacteria">bacteria</a> and <a href="Fungus" title="Fungus">fungi</a>, such as <a href="Auxin" title="Auxin">auxin</a> synthesis, protection against <a href="Abiotic_stress" title="Abiotic stress">abiotic stress</a>, and <a href="Nitrogen_fixation" title="Nitrogen fixation">nitrogen fixation</a>.<sup id="cite_ref-Taffner-2018_36-2" class="reference"><a href="#cite_note-Taffner-2018-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-44" class="reference"><a href="#cite_note-44"><span class="cite-bracket">[</span>44<span class="cite-bracket">]</span></a></sup> In some cases, key genes for plant growth and development, such as <a href="Plant_physiology" title="Plant physiology">metabolism</a> and <a href="Cell_wall" title="Cell wall">cell wall</a> synthesis, are more prevalent in archaea than bacteria.<sup id="cite_ref-Taffner-2018_36-3" class="reference"><a href="#cite_note-Taffner-2018-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup>
</p><p>Archaeal presence in the root microbiome can also be affected by plant hosts, which can change the diversity, presence, and health of archaeal communities.<sup id="cite_ref-Buée-2009_8-2" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Wang-2015_38-1" class="reference"><a href="#cite_note-Wang-2015-38"><span class="cite-bracket">[</span>38<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-45" class="reference"><a href="#cite_note-45"><span class="cite-bracket">[</span>45<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading3"><h3 id="Viruses">Viruses</h3></div>
<p>Viruses also infect plants via the roots; however, to penetrate the root tissues, they typically use vectors such as nematodes or fungi.<sup id="cite_ref-Mendes-2013_1-6" class="reference"><a href="#cite_note-Mendes-2013-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading2"><h2 id="Assembly_mechanisms">Assembly mechanisms</h2></div>
<p>There is an ongoing debate regarding what mechanisms are responsible for assembling individual microbes into <a href="Community_(ecology)" title="Community (ecology)">communities</a>. There are two primary competing hypotheses. One is that "everything is everywhere, but the environment selects," meaning <a href="Biotic_component" class="mw-redirect" title="Biotic component">biotic</a> and <a href="Abiotic_component" title="Abiotic component">abiotic</a> factors pose the only constraints, through <a href="Natural_selection" title="Natural selection">natural selection</a>, to which microbes colonize what <a href="Ecology#Physical_environments" title="Ecology">environments</a>. This is called the <a href="Niche_(ecology)" class="mw-redirect" title="Niche (ecology)">niche</a> hypothesis. Its counterpart is the hypothesis that neutral processes, such as distance and geographic barriers to <a href="Dispersal_(ecology)" class="mw-redirect" title="Dispersal (ecology)">dispersal</a>, control microbial community assembly when <a href="Taxon" title="Taxon">taxa</a> are equally <a href="Biological_fitness" class="mw-redirect" title="Biological fitness">fit</a> 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.<sup id="cite_ref-Nemergut-2013_7-1" class="reference"><a href="#cite_note-Nemergut-2013-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> 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.<sup id="cite_ref-Nemergut-2013_7-2" class="reference"><a href="#cite_note-Nemergut-2013-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup>
</p><p>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,<sup id="cite_ref-Nemergut-2013_7-3" class="reference"><a href="#cite_note-Nemergut-2013-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> particularly in roots. For this reason, only assembly mechanisms that fit within the niche hypothesis are discussed below.
</p><p>The taxa within root microbial communities seem to be partly drawn from the surrounding soil, though the relative abundance of various taxa may differ greatly from those found in bulk soil due to unique <a href="Niche_(ecology)" class="mw-redirect" title="Niche (ecology)">niches</a> in the root and rhizosphere.<sup id="cite_ref-Buée-2009_8-3" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup>
</p><p>Recent evidence shows that seed-transmitted bacteria contribute significantly to the composition of the root microbiome. In wheat, they can dominate over soil-derived microbes and structure the rhizosphere community through niche partitioning and facilitation.<sup id="cite_ref-46" class="reference"><a href="#cite_note-46"><span class="cite-bracket">[</span>46<span class="cite-bracket">]</span></a></sup> These bacteria possess traits that allow them to degrade root-derived compounds and support the growth of other microbes, highlighting the importance of seed microbiota in microbial succession and community assembly within the rhizosphere.
</p>
<div class="mw-heading mw-heading3"><h3 id="Biotic_assembly_mechanisms">Biotic assembly mechanisms</h3></div>
<p>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,<sup id="cite_ref-Buée-2009_8-4" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Marschner-2001_47-0" class="reference"><a href="#cite_note-Marschner-2001-47"><span class="cite-bracket">[</span>47<span class="cite-bracket">]</span></a></sup> and the rhizosphere, root surface, and root tissue are all associated with different communities,<sup id="cite_ref-Gottel-2011_2-1" class="reference"><a href="#cite_note-Gottel-2011-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Nguyen-2009_3-1" class="reference"><a href="#cite_note-Nguyen-2009-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> likely due to the unique chemistry and nutrient status of each of these regions, which differ from those of the bulk soil.<sup id="cite_ref-:0_48-0" class="reference"><a href="#cite_note-:0-48"><span class="cite-bracket">[</span>48<span class="cite-bracket">]</span></a></sup> For instance, root exudates provide specific carbon compounds that are enriched in the rhizosphere, selecting for microbial taxa with matching metabolic traits and shaping root-associated communities accordingly.<sup id="cite_ref-:0_48-1" class="reference"><a href="#cite_note-:0-48"><span class="cite-bracket">[</span>48<span class="cite-bracket">]</span></a></sup> Additionally, different plant species, and even different cultivars, harbor different microbial communities,<sup id="cite_ref-Dean-2014_9-1" class="reference"><a href="#cite_note-Dean-2014-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Dean-2014-2_10-1" class="reference"><a href="#cite_note-Dean-2014-2-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Marschner-2001_47-1" class="reference"><a href="#cite_note-Marschner-2001-47"><span class="cite-bracket">[</span>47<span class="cite-bracket">]</span></a></sup> probably due to host specific immune responses<sup id="cite_ref-Kogel-2006_4-4" class="reference"><a href="#cite_note-Kogel-2006-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> and differences in carbon root exudates.<sup id="cite_ref-49" class="reference"><a href="#cite_note-49"><span class="cite-bracket">[</span>49<span class="cite-bracket">]</span></a></sup> Host age affects root microbial community composition, likely for similar reasons as host identity.<sup id="cite_ref-Buée-2009_8-5" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> The identity of neighboring vegetation has also been shown to impact a host plant's root microbial community composition.<sup id="cite_ref-Dean-2014_9-2" class="reference"><a href="#cite_note-Dean-2014-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Dean-2014-2_10-2" class="reference"><a href="#cite_note-Dean-2014-2-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-50" class="reference"><a href="#cite_note-50"><span class="cite-bracket">[</span>50<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-51" class="reference"><a href="#cite_note-51"><span class="cite-bracket">[</span>51<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading3"><h3 id="Abiotic_assembly_mechanisms">Abiotic assembly mechanisms</h3></div>
<p>Abiotic mechanisms also affect root microbial community assembly<sup id="cite_ref-Dean-2014_9-3" class="reference"><a href="#cite_note-Dean-2014-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Dean-2014-2_10-3" class="reference"><a href="#cite_note-Dean-2014-2-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Hardoim-2011_11-1" class="reference"><a href="#cite_note-Hardoim-2011-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Egerton-Warburton-2007_12-1" class="reference"><a href="#cite_note-Egerton-Warburton-2007-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Tedersoo-2012_13-1" class="reference"><a href="#cite_note-Tedersoo-2012-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> because individual taxa have different optima along various <a href="Environmental_gradient" title="Environmental gradient">environmental gradients</a>, such as nutrient concentrations, pH, moisture, temperature, etc. In addition to chemical and climatic factors, soil structure and disturbance impact root biotic assembly.<sup id="cite_ref-Buée-2009_8-6" class="reference"><a href="#cite_note-Buée-2009-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup>
</p>
<div class="mw-heading mw-heading3"><h3 id="Succession">Succession</h3></div>
<p>The root microbiome is dynamic and fluid within the constraints imposed by the biotic and abiotic environment. As in <a href="Macroecology" title="Macroecology">macroecological</a> 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.<sup id="cite_ref-Nemergut-2013_7-4" class="reference"><a href="#cite_note-Nemergut-2013-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> While the effect of initial community on microbial <a href="Ecological_succession" title="Ecological succession">succession</a> has been studied in various environmental samples, <a href="Human_microbiome" title="Human microbiome">human microbiome</a>, and laboratory settings, it has yet to be studied in roots.
</p>
<div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2></div>
<ul><li><a href="Mangrove_root_microbiome" class="mw-redirect" title="Mangrove root microbiome">Mangrove root microbiome</a></li></ul>
<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>
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<li id="cite_note-50"><span class="mw-cite-backlink"><b><a href="#cite_ref-50">^</a></b></span> <span class="reference-text"><cite id="CITEREFBogarKennedy2013" class="citation journal cs1">Bogar LM, Kennedy PG (March 2013). <a rel="nofollow" class="external text" href="https://doi.org/10.1111%2F1574-6941.12032">"New wrinkles in an old paradigm: neighborhood effects can modify the structure and specificity of Alnus-associated ectomycorrhizal fungal communities"</a>. <i>FEMS Microbiology Ecology</i>. <b>83</b> (3): <span class="nowrap">767–</span>77. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2013FEMME..83..767B">2013FEMME..83..767B</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.1111%2F1574-6941.12032">10.1111/1574-6941.12032</a></span>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/23078526">23078526</a>.</cite></span>
</li>
<li id="cite_note-51"><span class="mw-cite-backlink"><b><a href="#cite_ref-51">^</a></b></span> <span class="reference-text"><cite id="CITEREFMeinhardtGehring2012" class="citation journal cs1">Meinhardt KA, Gehring CA (March 2012). "Disrupting mycorrhizal mutualisms: a potential mechanism by which exotic tamarisk outcompetes native cottonwoods". <i>Ecological Applications</i>. <b>22</b> (2): <span class="nowrap">532–</span>49. <a href="Bibcode_(identifier)" class="mw-redirect" title="Bibcode (identifier)">Bibcode</a>:<a rel="nofollow" class="external text" href="https://ui.adsabs.harvard.edu/abs/2012EcoAp..22..532M">2012EcoAp..22..532M</a>. <a href="Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1890%2F11-1247.1">10.1890/11-1247.1</a>. <a href="PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/22611852">22611852</a>.</cite></span>
</li>
</ol></div>
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</style></div><div role="navigation" class="navbox" aria-labelledby="Microorganisms250" style="padding:3px"><table class="nowraplinks hlist mw-collapsible autocollapse navbox-inner" style="border-spacing:0;background:transparent;color:inherit"><tbody><tr><th scope="col" class="navbox-title" colspan="3"><div id="Microorganisms250" style="font-size:114%;margin:0 4em"><a href="Microorganism" title="Microorganism">Microorganisms</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Microorganism" title="Microorganism">Groups</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Archaea" title="Archaea">Archaea</a></li>
<li><a href="Bacteria" title="Bacteria">Bacteria</a></li>
<li><a href="Cyanobacteria" title="Cyanobacteria">Cyanobacteria</a></li>
<li><a href="Fungus" title="Fungus">Fungi</a></li>
<li><a href="Nanobacterium" title="Nanobacterium">Nanobacterium</a></li>
<li><a href="Prokaryote" title="Prokaryote">Prokaryote</a></li>
<li><a href="Protist" title="Protist">Protist</a></li>
<li><a href="Protozoa" title="Protozoa">Protozoa</a></li>
<li><a href="Virus" title="Virus">Virus</a></li></ul>
</div></td><td class="noviewer navbox-image" rowspan="9" style="width:1px;padding:0 0 0 2px"><div><span typeof="mw:File"></span></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Microbiology" title="Microbiology">Microbiology</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Microbial_biogeography" title="Microbial biogeography">Microbial biogeography</a></li>
<li><a href="Microbial_genetics" title="Microbial genetics">Microbial genetics</a></li>
<li><a href="Microbial_intelligence" title="Microbial intelligence">Microbial intelligence</a></li>
<li><a href="Microbial_metabolism" title="Microbial metabolism">Microbial metabolism</a></li>
<li><a href="Microbial_phylogenetics" title="Microbial phylogenetics">Microbial phylogenetics</a></li>
<li><a href="Microbial_population_biology" title="Microbial population biology">Microbial population biology</a></li>
<li><a href="Mycology" title="Mycology">Mycology</a></li>
<li><a href="Virology" title="Virology">Virology</a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Motion</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Bacterial_motility" title="Bacterial motility">Bacterial motility</a>
<ul><li><a href="Run-and-tumble_motion" title="Run-and-tumble motion">run-and-tumble</a></li>
<li><a href="Twitching_motility" title="Twitching motility">twitching</a></li>
<li><a href="Gliding_motility" title="Gliding motility">gliding</a></li></ul></li>
<li><a href="Protist_locomotion" title="Protist locomotion">Protist locomotion</a>
<ul><li><a href="Amoeboid_movement" title="Amoeboid movement">amoeboids</a></li></ul></li>
<li><a href="Bacteria_collective_motion" title="Bacteria collective motion">Bacteria collective motion</a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Microbial_ecology" title="Microbial ecology">Ecology</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Biofilm" title="Biofilm">Biofilm</a></li>
<li><a href="Biological_pump" title="Biological pump">Biological pump</a></li>
<li><a href="Kill_the_Winner_hypothesis" title="Kill the Winner hypothesis">Kill the Winner hypothesis</a></li>
<li><a href="Microbial_consortium" title="Microbial consortium">Microbial consortium</a></li>
<li><a href="Microbial_cooperation" title="Microbial cooperation">Microbial cooperation</a></li>
<li><a href="Microbial_biodegradation" title="Microbial biodegradation">Microbial biodegradation</a></li>
<li><a href="Microbial_ecology" title="Microbial ecology">Microbial ecology</a></li>
<li><a href="Microbial_cyst" title="Microbial cyst">Microbial cyst</a></li>
<li><a href="Microbial_food_web" title="Microbial food web">Microbial food web</a>
<ul><li><a href="Microbial_loop" title="Microbial loop">microbial loop</a></li>
<li><a href="Viral_shunt" title="Viral shunt">viral shunt</a></li></ul></li>
<li><a href="Microbial_mat" title="Microbial mat">Microbial mat</a></li>
<li><a href="Microbial_synergy" title="Microbial synergy">Microbial synergy</a></li>
<li><a href="Microbiome" title="Microbiome">Microbiome</a>
<ul><li><a href="Microbiota" title="Microbiota">microbiota</a></li>
<li><a href="Holobiont" title="Holobiont">holobiont</a></li></ul></li>
<li><a href="Quorum_sensing" title="Quorum sensing">Quorum sensing</a></li>
<li><a href="Host_microbe_interactions_in_Caenorhabditis_elegans" title="Host microbe interactions in Caenorhabditis elegans">Host microbe interactions in <i>Caenorhabditis elegans</i></a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Plants</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Plant_microbiome" title="Plant microbiome">Plant microbiome</a></li>
<li><a href="Seagrass_microbiome" class="mw-redirect" title="Seagrass microbiome">Seagrass microbiome</a></li>
<li><a href="Soil_microbiology" title="Soil microbiology">Soil microbiology</a></li>
<li><a href="Spermosphere" title="Spermosphere">Spermosphere</a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Marine</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Marine_microorganisms" title="Marine microorganisms">Marine microorganisms</a></li>
<li><a href="Marine_viruses" title="Marine viruses">Marine viruses</a></li>
<li><a href="Marine_prokaryotes" title="Marine prokaryotes">Marine prokaryotes</a></li>
<li><a href="Marine_protists" title="Marine protists">Marine protists</a></li>
<li><a href="Microalgae" title="Microalgae">Microalgae</a></li>
<li><a href="Antarctic_microorganism" title="Antarctic microorganism">Antarctic microorganism</a></li>
<li><a href="Coral_microbiome" class="mw-redirect" title="Coral microbiome">Coral microbiome</a></li>
<li><a href="Hydrothermal_vent_microbial_communities" title="Hydrothermal vent microbial communities">Hydrothermal vent microbial communities</a></li>
<li><a href="Marine_microbial_symbiosis" title="Marine microbial symbiosis">Marine microbial symbiosis</a></li>
<li><a href="Microbial_oxidation_of_sulfur" title="Microbial oxidation of sulfur">Microbial oxidation of sulfur</a></li>
<li><a href="Phycosphere" title="Phycosphere">Phycosphere</a></li>
<li><a href="Picoeukaryote" title="Picoeukaryote">Picoeukaryote</a></li>
<li><a href="International_Census_of_Marine_Microbes" title="International Census of Marine Microbes">International Census of Marine Microbes</a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Human related</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Human_interactions_with_microbes" title="Human interactions with microbes">Microbes in human culture</a></li>
<li><a href="Microbiomes_of_the_built_environment" title="Microbiomes of the built environment">Microbiomes of the built environment</a></li>
<li><a href="Food_microbiology" title="Food microbiology">Food microbiology</a></li>
<li><a href="Microbial_oil" title="Microbial oil">Microbial oil</a></li>
<li><a href="Microbial_symbiosis_and_immunity" title="Microbial symbiosis and immunity">Microbial symbiosis and immunity</a></li>
<li><a href="Nylon-eating_bacteria" title="Nylon-eating bacteria">Nylon-eating</a></li>
<li><a href="Human_microbiome" title="Human microbiome">Human microbiome</a>
<ul><li><a href="Asthma-related_microbes" title="Asthma-related microbes">asthma</a></li>
<li><a href="Dysbiosis" title="Dysbiosis">dysbiosis</a></li>
<li><a href="Fecal_microbiota_transplant" title="Fecal microbiota transplant">fecal</a></li>
<li><a href="Gut_microbiota" title="Gut microbiota">gut</a></li>
<li><a href="Lung_microbiota" title="Lung microbiota">lung</a></li>
<li><a href="Oral_microbiology" title="Oral microbiology">mouth</a></li>
<li><a href="Skin_flora" title="Skin flora">skin</a></li>
<li><a href="Vaginal_flora" title="Vaginal flora">vagina</a>
<ul><li><a href="Vaginal_flora_in_pregnancy" title="Vaginal flora in pregnancy">in pregnancy</a></li></ul></li>
<li><a href="Placental_microbiome" title="Placental microbiome">placenta</a></li>
<li><a href="Uterine_microbiome" title="Uterine microbiome">uterus</a></li></ul></li>
<li><a href="Human_Microbiome_Project" title="Human Microbiome Project">Human Microbiome Project</a></li>
<li><a href="Protein_production" title="Protein production">Protein production</a></li>
<li><a href="Synthetic_microbial_consortia" title="Synthetic microbial consortia">Synthetic microbial consortia</a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Techniques</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Dark-field_microscopy" title="Dark-field microscopy">Dark-field microscopy</a></li>
<li><a href="DNA_sequencing" title="DNA sequencing">DNA sequencing</a></li>
<li><a href="Impedance_microbiology" title="Impedance microbiology">Impedance microbiology</a></li>
<li><a href="Microbial_cytology" title="Microbial cytology">Microbial cytology</a></li>
<li><a href="Microbial_DNA_barcoding" title="Microbial DNA barcoding">Microbial DNA barcoding</a></li>
<li><a href="Microbiological_culture" title="Microbiological culture">Microbiological culture</a></li>
<li><a href="Staining" title="Staining">Staining</a></li></ul>
</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Other</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em">
<ul><li><a href="Bioremediation" title="Bioremediation">Bioremediation</a></li>
<li><a href="Deep_biosphere" title="Deep biosphere">Deep biosphere</a></li>
<li><a href="Microbial_dark_matter" title="Microbial dark matter">Microbial dark matter</a></li>
<li><a href="Microswimmer" title="Microswimmer">Microswimmer</a>
<ul><li><a href="Biohybrid_microswimmer" title="Biohybrid microswimmer">biohybrid</a></li></ul></li>
<li><a href="Lines_on_the_Antiquity_of_Microbes" title="Lines on the Antiquity of Microbes">Lines on the Antiquity of Microbes</a></li>
<li><a href="Microbially_induced_sedimentary_structure" title="Microbially induced sedimentary structure">Microbially induced sedimentary structure</a></li>
<li><a href="Omics" title="Omics">Omics</a></li>
<li><a href="Physical_factors_affecting_microbial_life" title="Physical factors affecting microbial life">Physical factors affecting microbial life</a></li>
<li><a href="Siderophore" title="Siderophore">Siderophore</a></li></ul>
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