Root microbiome

[1] Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi, and archaea.

[1] Some pathogenic bacteria that can be carried over to humans, such as Salmonella, enterohaemorhagic Escherichia coli, Burkholderia cenocepacia, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia, can also be detected in root microbiomes and other plant tissues.

[8] Evidence suggests both biotic (such as host identity and plant neighbor) and abiotic (such as soil structure and nutrient availability) factors affect community composition.

Because they are multicellular, fungi can extend hyphae from nutrient exchange organs within host cells into the surrounding rhizosphere and bulk soil.

[25] Mycorrhizal (from Greek) literally means "fungus roots" and defines symbiotic interaction between plants and fungi.

Rhizobia and dark septate endophytes (which produce melanin, an antioxidant that may provide resilience against a variety of environmental stresses[27]) are examples.

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.

Bacteria attach to roots in a biphasic mechanism with two steps—first weak, non-specific binding, then a strong irreversible residence phase.

[32][39][40][41] Archaeal phyla found in the root microbiome include Euryarchaeota,[32][40][42] Nitrososphaerota (formerly Thaumarchaeota),[32][42] and Thermoproteota (formerly Crenarchaeota).

[40] The presence and relative abundance of archaea in various environments suggest that they likely play an important role in the root microbiome.

[32] Archaea have been found to promote plant growth and development, provide stress tolerance, improve nutrient uptake, and protect against pathogens.

[32][36][43] For example, Arabidopsis thaliana colonized with an ammonia-oxidizing soil archaea, Nitrosocosmicus oleophilius, exhibited increased shoot weight, photosynthetic activity, and immune response.

[43] Examination of microbial communities in soil and roots has identified archaeal organisms and genes with functions similar to that of bacteria and fungi, such as auxin synthesis, protection against abiotic stress, and nitrogen fixation.

[36][44] In some cases, key genes for plant growth and development, such as metabolism and cell wall synthesis, are more prevalent in archaea than bacteria.

Its counterpart is the hypothesis that neutral processes, such as distance and geographic barriers to dispersal, control microbial community assembly when taxa are equally fit within an environment.

[8] The identity of neighboring vegetation has also been shown to impact a host plant's root microbial community composition.

[9][10][48][49] Abiotic mechanisms also affect root microbial community assembly[9][10][11][12][13] because individual taxa have different optima along various environmental gradients, such as nutrient concentrations, pH, moisture, temperature, etc.

In addition to chemical and climatic factors, soil structure and disturbance impact root biotic assembly.

Sunlight and carbon dioxide from the atmosphere are absorbed by the leaves in the plant and converted to fixed carbon. This carbon travels down into the roots of the plant, where some travels back up to the leaves. The fixed carbon traveling to the root is radiated outward into the surrounding soil where microbes use it as food for growth. In return, microbes attach to the plant root where it improves the roots access to nutrients and its resistance to environmental stress and pathogens. In specific plant/root symbiotic relationships, the plant root secretes flavonoids into the soil which is sensed by microbes, where these microbes release nod factors to the plant root which promotes the infection of the plant root. These unique microbes carry out nitrogen fixation in root nodules, which supplies nutrients to the plant.