Phytobiome

The Phytobiome is a term that relates to a plant (phyto) in a specific ecological area (biome). It includes the plant itself, the environment and all micro- and macro-organisms living in, on, or around the plant. These organisms include bacteria, archaea, fungi, protists, insects, animals and other plants. The environment includes the soil, air and climate. Examples of ecological areas are fields, rangelands, forests.[1] Knowledge of the interactions within a phytobiome can be used to create tools for agriculture, crop management,[2] increased health, preservation, productivity, and sustainability of cropping and forest systems.[3][4]

"Phytobiomes" redirects here. For the journal, see Phytobiomes (journal).

Signaling
Environments within the Phytobiome

Diversity

The microbial community within the phytobiome is perhaps one of the most rich and diverse microbiomes on Earth. Plants form associations with billions of organisms across every kingdom of life. Recent metagenomic and metatranscriptomic approaches have allowed scientists to discover novel taxonomic species that are not easily cultured in a laboratory.

Bacteria

Recent research has shown that inter-kingdom communication between organisms is essential for proper phytobiome function.[5] There are numerous physical and chemical signals such as secreted lipids, peptides and polysaccharides that allow organisms to recognize and interact within the phytobiome. Bacteria are known to produce quorum sensing molecules such as homoserine lactones (HSLs), lipid-like diffusable factors and signaling peptides that mediate plant-bacteria interactions such as colonization.[5] HSLs have been are reportedly produced by a large number of bacteria found in the rhizosphere.[6] Plant growth promoting bacteria (PGPBs) often produce Nod factors (nodulation factors) that initiate nodule formation in plants.[5] In addition to plant-bacterial interactions, bacteria often secrete bactericidal or fungicidal compounds into the phytobiome to reduce local competition for niches and resources.[5] Additionally, organisms that feed on bacteria such as some species of algae and protists are attracted to these small signaling molecules.[5]

Phages

Bacteriophages also play a critical role in the phytobiome through predator-prey interactions. Bacteriophages use a signaling peptides such as arbitrium to mediate the initiation of cell lysis and lysogeny in the host cell.[7]

Fungi

Fungi communicate in the phytobiome through chemical signaling to aid in sexual reproduction, sporulation, cell-to-cell recognition and antibiosis; however, only a fraction of these chemicals have been studied for their function.[5] Mycorrhizal fungi establish symbiotic relationships with plants through the production of Myc factors, or chitooligosaccharides that are recognized by receptors in the plant.[8] Nematode-trapping fungi often utilize fungal signaling molecules to initiate morphogensis towards prey.[5] Other organisms can interfere with fungal signaling, such as plant-produced oxylipins that mimic fungal signaling molecules and can regulate fungal development or reduce virulence.[5] Multiple spceis of bacteria, insects and nematodes have all been reported to respond to fungal signaling compounds.[8]

Nematodes

Very little is known about nematode communication within the phytobiome. Plant-pathogenic nematodes often communicate through production of pheromones.[5] Plants can detect these compounds and induce defense pathways.[5] Nematodes also produce plant hormones such as cytokinins that aid in the establishment of association with plants.[5]

Protists

Perhaps even less is known about the ecological role of protists and viruses within the phytobiome. Some amoebae species use cyclic nucleotides or peptide signals to adapt social behavior.[5] Phytohormones produced by algae-associated bacteria can greatly impact microalgae populations in the soil.[5] The presence of amoeba can also trigger the bacterium P. fluorescens to produce anti-amoebal toxins.[9]

Insects

Insects communicate to transfer information regarding external threats, social status, food availability and mating through the production of volatile pheromones, also known as semiochemicals.[5] This has made pheromones a subject of research since the 1950s for various applications in agriculture and insect-vectored diseases such as malaria.[5] Plants can have profound impacts on insect pheromone production. Rattlebox plants produce various alkaloid compounds that insects use as a precursor for sex pheromone synthesis.[5] Many plant species have evolved production of volatile chemicals that interfere with pheromone signaling, often through inhibition of proper olfactory neuron function.[5] Bacteria and fungi can also produce volatile chemicals that affect insect behavior.[10]

Plants

The presence of plants and their communication with other community members fundamentally shapes the phytobiome. Root exudates contain numerous sugars, amino acids, polysaccharides and secondary metabolites.[5] The production of these exudates is heavily influenced by environmental factors and plant physiology and can alter the community composition of the rhizosphere and rhizoplain.[5]The secretion of flavonoids helps to recruit Rhizobia bacteria that form a mutualistic symbiosis with numerous plant species.[5] Rhizobia can also recognize other plant compounds such as betaines, aldonic acids and jasmonic acid.[8] These signal molecules can have multiple or even counteracting effects. For example, plant cutins trigger arbuscular mycorrhizal colonization and symbiosis but can also be recognized by plant-pathogenic oomycetes and trigger pathogenesis.[11] Plant volatile chemicals also attract herbivores, pollinators and seed carriers.

When plants recognize the presence of microbes, they often activate the production of phytohormone signals that are transported throughout the plant. Plants respond to pathogens and herbivores through production of hormones including salicylic acid, jasmonic acid and ethylene.[12] In addition, many phytohormones that function in abiotic stress tolerance or plant growth also trigger responses with the microbial community. The production of salicylic acid in Arabidopsis was shown to influence the root microbiome composition by acting as a signal or carbon source.[13] Secretion of strigolactone is known to stimulate spore germination and Myc factor production in arbuscular mycorrhizal fungi.[5]

The microbial community can also manipulate phytohormone function or the production of specific phytohormones in plants.

Research

In 2015 the American Phytopathological Society (APS) launched a research framework, the Phytobiomes Initiative, to facilitate the organization of research into phytobiome.[14] As part of this effort, in 2016 it launched Phytobiomes Journal, an open-access journal. The journal focuses on transdisciplinary research that impacts the entire plant ecosystem.[15] An overall research strategy has been published in the Phytobiomes Roadmap, a document developed by a group of scientific societies, companies, research institutes, and governmental agencies. It is intended to present a strategic plan to study phytobiomes and propose an action plan to apply phytobiome studies.[16][17] The connected Phytobiomes Alliance is an international, nonprofit consortium of academic institutions, large and small companies, and governmental agencies coordinating public-private research projects on various aspects of agriculturally relevant phytobiomes.[18]

See also

References
  1. "About Phytobiomes". Phytobiomes Alliance.
  2. Beans C (August 2017). "Core Concept: Probing the phytobiome to advance agriculture". Proceedings of the National Academy of Sciences of the United States of America. 114 (34): 8900–8902. doi:10.1073/pnas.1710176114. PMC 5576833. PMID 28831027.CS1 maint: ref=harv (link)
  3. "Studying interconnected communities of plants, microbes and other organisms in agriculture can unlock benefits for producers, consumers". Iowa State University - News Service. 4 March 2016. Retrieved 20 June 2017.
  4. Hart J (7 November 2016). "Can knowing more about soil microbes be used to make better crop yields?". Southeast FarmPress.
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  6. Schaefer AL, Lappala CR, Morlen RP, Pelletier DA, Lu TY, Lankford PK, et al. (September 2013). "LuxR- and luxI-type quorum-sensing circuits are prevalent in members of the Populus deltoides microbiome". Applied and Environmental Microbiology. 79 (18): 5745–52. doi:10.1128/AEM.01417-13. PMC 3754149. PMID 23851092.
  7. Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, et al. (January 2017). "Communication between viruses guides lysis-lysogeny decisions". Nature. 541 (7638): 488–493. Bibcode:2017Natur.541..488E. doi:10.1038/nature21049. PMC 5378303. PMID 28099413.
  8. Smith DL, Praslickova D, Ilangumaran G (2015). "Inter-organismal signaling and management of the phytomicrobiome". Frontiers in Plant Science. 6: 722. doi:10.3389/fpls.2015.00722. PMC 4568390. PMID 26442036.
  9. Jousset A, Rochat L, Scheu S, Bonkowski M, Keel C (August 2010). "Predator-prey chemical warfare determines the expression of biocontrol genes by rhizosphere-associated Pseudomonas fluorescens". Applied and Environmental Microbiology. 76 (15): 5263–8. doi:10.1128/AEM.02941-09. PMC 2916451. PMID 20525866.
  10. Davis TS, Crippen TL, Hofstetter RW, Tomberlin JK (July 2013). "Microbial volatile emissions as insect semiochemicals". Journal of Chemical Ecology. 39 (7): 840–59. doi:10.1007/s10886-013-0306-z. PMID 23793954. S2CID 4307691.
  11. Wang E, Schornack S, Marsh JF, Gobbato E, Schwessinger B, Eastmond P, et al. (December 2012). "A common signaling process that promotes mycorrhizal and oomycete colonization of plants". Current Biology. 22 (23): 2242–6. doi:10.1016/j.cub.2012.09.043. PMID 23122843.
  12. Pieterse CM, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SC (2012-10-11). "Hormonal modulation of plant immunity". Annual Review of Cell and Developmental Biology. 28 (1): 489–521. doi:10.1146/annurev-cellbio-092910-154055. hdl:1874/274421. PMID 22559264. S2CID 18180536.
  13. Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, et al. (August 2015). "PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa". Science. 349 (6250): 860–4. doi:10.1126/science.aaa8764. PMID 26184915.
  14. Ledford H (July 2015). "Plant denizens get the big-science treatment". Nature. 523 (7559): 137–8. Bibcode:2015Natur.523..137L. doi:10.1038/523137a. PMID 26156352.
  15. "Phytobiomes - An Open Access Transdisciplinary Journal of Sustainable Plant Productivity". APS Journals. Retrieved 20 June 2017.
  16. "Phytobiomes Roadmap" (PDF). www.phytobiomes.org. Retrieved 3 June 2017.
  17. "Roadmap Launched for Phytobiomes Research". Seedworld.com. 2016-02-26.
  18. / "Phytobiomes Alliance - Home" Check |url= value (help). Phytobiomes Alliance. Retrieved 20 June 2017.
  • "Phytobiomes". phytobiomes.org. 2018-06-21. Retrieved 2018-06-21.
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