Root microbiome

The root microbiome is the dynamic community of microorganisms associated with plant roots. 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. The microbial communities inside the root and in the rhizosphere are distinct from each other,[1] and from the microbial communities of bulk soil,[2] although there is some overlap in species composition. Root microbiota affect plant host fitness and productivity 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,[3] or may change the nature of their interaction (along the mutualist-parasite continuum) within a single host as environmental conditions or host health change.[4]

Despite the potential importance of the root microbiome for plants and ecosystems, our understanding of how root microbial communities are assembled is in its infancy.[5][6] This is in part because until recent advances in sequencing technologies, root microbes were difficult to study due to high species diversity, the large number of cryptic species, and the fact that most species have yet to be retrieved in culture.[7] Evidence suggests both biotic (such as host identity and plant neighbor) and abiotic (such as soil structure and nutrient availability) factors affect community composition.[8][9][10][11][12]

Function

Types of Symbioses

Root associated microbes include fungi, bacteria, and archaea living within or on the surface of roots, as well as in the rhizosphere. Symbionts associated with plant roots subsist off of photosynthetic 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,[13][14][15] produce plant-growth regulators,[16] improve environmental stress tolerance of their host,[17][18][19] induce host defenses and systemic resistance against pests or pathogens,[20][21][22] or be pathogenic.[23] 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, many may behave one way or the other depending on the host species with which it is associated, environmental conditions, and host health.[3] A host’s immune response controls symbiont infection and growth rates.[3] 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.[3]

Composition

Roots are colonized by fungi, bacteria and archaea. Because they are multicellular, fungi can extend hyphae 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, but external hyphae can also include other endophytic fungi. Mycorrhizal fungi can extend a great distance into bulk soil,[4] 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.[13] In return, plants may allocate ~20-40% of their carbon to mycorrhizae.[24]

Mycorrhizae

Main article: Mycorrhiza

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.[4] The main groups include ectomycorrhizae, arbuscular mycorhizae, ericoid mycorrhizae, orchid mycorrhizae, and monotropoid mycorrhizae. Monotropoid mycorrhizae are associated with plants in the monotropaceae, which lack chlorophyll. Many Orchids 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.[4] Achlorophyllous plants forming these types of mycorrhizal associations are called mycoheterotrophs.

Endophytes

Main article: Endophyte

Endophytes are bacteria or fungi that live within plant tissue. They may colonize inter-cellular spaces, the root cells themselves, or both. Rhizobia and dark septate endophytes (which produce melanin, an antioxidant that may provide resilience against a variety of environmental stresses[25]) are famous examples.

Archaea

Main article: Archaea

Archaea are traditionally thought of as microbes belonging to extreme environments. Though they are found in plant roots, little is known about their effect on plant health or their role in the root microbiome.[7]

Assembly Mechanisms

There is an ongoing debate regarding what mechanisms are responsible for assembling individual microbes into communities. There are two primary competing hypotheses. One is that "everything is everywhere, but the environment selects," meaning biotic and abiotic factors pose the only constraints, through natural selection, to which microbes colonize what environments. This is called the niche hypothesis, and 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. In this hypothesis, differences between individual taxa in modes and reach of dispersal explain the differences in microbial communities of different environments.[6] 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.[6]

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,[6] 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.[7]

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,[7][26] and the rhizosphere, root surface, and root tissue are all associated with different communities,[1][2] 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,[8][9][26] probably due to host specific immune responses[3] and differences in carbon root exudates.[27] Host age affects root microbial community composition, likely for similar reasons as host identity.[7] The identity of neighboring vegetation has also been shown to impact a host plant's root microbial community composition.[8][9][28][29]

Abiotic Assembly Mechanisms

Abiotic mechanisms also affect root microbial community assembly[8][9][10][11][12] 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.[7]

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 therefor how the community responds to changes in the host or environment.[6] While the effect of initial community on microbial succession has been studied in various environmental samples, human microbiome, and laboratory settings, it has yet to be studied in roots.

References

  1. 1 2 Gottel NR, Castro HF, Kerley M, et al. (September 2011). "Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types". Applied and Environmental Microbiology. 77 (17): 5934–44. doi:10.1128/AEM.05255-11. PMC 3165402Freely accessible. PMID 21764952.
  2. 1 2 Nguyen, Christophe (2009), "Rhizodeposition of Organic C by Plant: Mechanisms and Controls", Sustainable Agriculture, pp. 97–123, doi:10.1007/978-90-481-2666-8_9, ISBN 978-90-481-2665-1
  3. 1 2 3 4 5 Kogel KH, Franken P, Hückelhoven R (August 2006). "Endophyte or parasite--what decides?". Current Opinion in Plant Biology. 9 (4): 358–63. doi:10.1016/j.pbi.2006.05.001. PMID 16713330.
  4. 1 2 3 4 Smith, Sally E.; Read, David J. (2010). Mycorrhizal symbiosis (3rd ed.). New York, NY: Academic Press. ISBN 978-0-08-055934-6.
  5. ↑ Kristin, Aleklett; Miranda, Hart (2013). "The root microbiota—a fingerprint in the soil?". Plant and Soil. 370 (1–2): 671–86. doi:10.1007/s11104-013-1647-7.
  6. 1 2 3 4 5 Nemergut DR, Schmidt SK, Fukami T, et al. (September 2013). "Patterns and processes of microbial community assembly". Microbiology and Molecular Biology Reviews. 77 (3): 342–56. doi:10.1128/MMBR.00051-12. PMC 3811611Freely accessible. PMID 24006468.
  7. 1 2 3 4 5 6 Buée, M.; De Boer, W.; Martin, F.; van Overbeek, L.; Jurkevitch, E. (2009). "The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors". Plant and Soil. 321 (1–2): 189–212. doi:10.1007/s11104-009-9991-3.
  8. 1 2 3 4 Dean SL, Farrer EC, Taylor DL, Porras-Alfaro A, Suding KN, Sinsabaugh RL (March 2014). "Nitrogen deposition alters plant-fungal relationships: linking belowground dynamics to aboveground vegetation change". Molecular Ecology. 23 (6): 1364–78. doi:10.1111/mec.12541. PMID 24112704.
  9. 1 2 3 4 Dean SL, Farrer EC, Porras-Alfaro A, Suding KN, Sinsabaugh RL (2014). "Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors". Environmental Microbiology Reports. doi:10.1111/1758-2229.12194.
  10. 1 2 Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, van Overbeek LS, van Elsas JD (July 2011). "Rice root-associated bacteria: insights into community structures across 10 cultivars". FEMS Microbiology Ecology. 77 (1): 154–64. doi:10.1111/j.1574-6941.2011.01092.x. PMID 21426364.
  11. 1 2 Egerton-Warburton, Louise M.; Johnson, Nancy Collins; Allen, Edith B. (November 2007). "Mycorrhizal Community Dynamics following Nitrogen Fertilization: A Cross-Site Test in Five Grasslands". Ecological Monographs. 77 (4): 527–44. doi:10.1890/06-1772.1. JSTOR 27646105.
  12. 1 2 Tedersoo L, Bahram M, Toots M, et al. (September 2012). "Towards global patterns in the diversity and community structure of ectomycorrhizal fungi". Molecular Ecology. 21 (17): 4160–70. doi:10.1111/j.1365-294X.2012.05602.x. PMID 22568722.
  13. 1 2 van der Heijden MG, Bardgett RD, van Straalen NM (March 2008). "The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems". Ecology Letters. 11 (3): 296–310. doi:10.1111/j.1461-0248.2007.01139.x. PMID 18047587.
  14. ↑ Marschner, Petra; Crowley, David; Rengel, Zed (2011). "Rhizosphere interactions between microorganisms and plants govern iron and phosphorus acquisition along the root axis – model and research methods". Soil Biology and Biochemistry. 43 (5): 883–94. doi:10.1016/j.soilbio.2011.01.005.
  15. ↑ Green, Laura E.; Porras-Alfaro, Andrea; Sinsabaugh, Robert L. (September 2008). "Translocation of Nitrogen and Carbon Integrates Biotic Crust and Grass Production in Desert Grassland". Journal of Ecology. 96 (5): 1076–85. doi:10.1111/j.1365-2745.2008.01388.x. JSTOR 20143553.
  16. ↑ Lugtenberg B, Kamilova F (2009). "Plant-growth-promoting rhizobacteria". Annual Review of Microbiology. 63: 541–56. doi:10.1146/annurev.micro.62.081307.162918. PMID 19575558.
  17. ↑ Latch, Garrick C.M. (1993). "Physiological interactions of endophytic fungi and their hosts. Biotic stress tolerance imparted to grasses by endophytes". Agriculture, Ecosystems & Environment. 44 (1–4): 143–56. doi:10.1016/0167-8809(93)90043-O.
  18. ↑ Rodriguez R, Redman R (2008). "More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis". Journal of Experimental Botany. 59 (5): 1109–14. doi:10.1093/jxb/erm342. PMID 18267941.
  19. ↑ Lau JA, Lennon JT (October 2011). "Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits". The New Phytologist. 192 (1): 215–24. doi:10.1111/j.1469-8137.2011.03790.x. PMID 21658184.
  20. ↑ Porras-Alfaro A, Bayman P (2011). "Hidden fungi, emergent properties: endophytes and microbiomes". Annual Review of Phytopathology. 49: 291–315. doi:10.1146/annurev-phyto-080508-081831. PMID 19400639.
  21. ↑ Doornbos, Rogier F.; van Loon, Leendert Cornelis; Bakker, Peter A. H. M. (2011). "Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review". Agronomy for Sustainable Development. 32 (1): 227–43. doi:10.1007/s13593-011-0028-y.
  22. ↑ Bakker, Peter A.H.M.; Doornbos, Rogier F.; Zamioudis, Christos; Berendsen, Roeland L.; Pieterse, Corne M.J. (2013). "Induced Systemic Resistance and the Rhizosphere Microbiome". The Plant Pathology Journal. 29 (2): 136–43. doi:10.5423/PPJ.SI.07.2012.0111.
  23. ↑ Packer A, Clay K (March 2000). "Soil pathogens and spatial patterns of seedling mortality in a temperate tree". Nature. 404 (6775): 278–81. Bibcode:2000Natur.404..278P. doi:10.1038/35005072. PMID 10749209.
  24. ↑ Smith, Sally E.; Read, David J. (1996). Mycorrhizal Symbiosis (2nd ed.). New York, NY: Academic Press. ISBN 978-0-08-053719-1.
  25. ↑ Jumpponen, Ari; Trappe, James M. (October 1998). "Dark Septate Endophytes: A Review of Facultative Biotrophic Root-Colonizing Fungi". New Phytologist. 140 (2): 295–310. doi:10.1046/j.1469-8137.1998.00265.x. JSTOR 2588371.
  26. 1 2 Marschner, P; Yang, C.-H; Lieberei, R; Crowley, D.E (2001). "Soil and plant specific effects on bacterial community composition in the rhizosphere". Soil Biology and Biochemistry. 33 (11): 1437–45. doi:10.1016/S0038-0717(01)00052-9.
  27. ↑ Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM (February 2008). "Root exudates regulate soil fungal community composition and diversity". Applied and Environmental Microbiology. 74 (3): 738–44. doi:10.1128/AEM.02188-07. PMC 2227741Freely accessible. PMID 18083870.
  28. ↑ Bogar LM, Kennedy PG (March 2013). "New wrinkles in an old paradigm: neighborhood effects can modify the structure and specificity of Alnus-associated ectomycorrhizal fungal communities". FEMS Microbiology Ecology. 83 (3): 767–77. doi:10.1111/1574-6941.12032. PMID 23078526.
  29. ↑ Meinhardt KA, Gehring CA (March 2012). "Disrupting mycorrhizal mutualisms: a potential mechanism by which exotic tamarisk outcompetes native cottonwoods". Ecological Applications. 22 (2): 532–49. doi:10.1890/11-1247.1. PMID 22611852.
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