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http://dx.doi.org/10.5423/PPJ.RW.05.2022.0065

Roads to Construct and Re-build Plant Microbiota Community  

Kim, Da-Ran (Research Institute of Life Sciences (RILS), Gyeongsang National University)
Kwak, Youn-Sig (Research Institute of Life Sciences (RILS), Gyeongsang National University)
Publication Information
The Plant Pathology Journal / v.38, no.5, 2022 , pp. 425-431 More about this Journal
Abstract
Plant microbiota has influenced plant growth and physiology significantly. Plant and plant-associated microbes have flexible interactions that respond to changes in environmental conditions. These interactions can be adjusted to suit the requirements of the microbial community or the host physiology. In addition, it can be modified to suit microbiota structure or fixed by the host condition. However, no technology is realized yet to control mechanically manipulated plant microbiota structure. Here, we review step-by-step plant-associated microbial partnership from plant growth-promoting rhizobacteria to the microbiota structural modulation. Glutamic acid enriched the population of Streptomyces, a specific taxon in anthosphere microbiota community. Additionally, the population density of the microbes in the rhizosphere was also a positive response to glutamic acid treatment. Although many types of research are conducted on the structural revealing of plant microbiota, these concepts need to be further understood as to how the plant microbiota clusters are controlled or modulated at the community level. This review suggests that the intrinsic level of glutamic acid in planta is associated with the microbiota composition that the external supply of the biostimulant can modulate.
Keywords
beneficial microbe; microbial engineering; microbiome; Streptomyces;
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1 Bais, H. P., Weir, T. L., Perry, L. G., Gilroy, S. and Vivanco, J. M. 2006. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu. Rev. Plant Biol. 57:233-266.   DOI
2 Beans, C. 2017. Core concept: probing the phytobiome to advance agriculture. Proc. Natl. Acad. Sci. U. S. A. 114:8900-8902.   DOI
3 Behie, S. W., Bonet, B., Zacharia, V. M., McClung, D. J. and Traxler, M. F. 2017. Molecules to ecosystems: actinomycete natural products in situ. Front. Microbiol. 7:2149.
4 Hernandez-Leon, R., Rojas-Solis, D., Contreras-Perez, M., del Carmen Orozco-Mosqueda, M., Macias-Rodriguez, L. I., Reyes-de la Cruz, H., Valencia-Cantero, E. and Santoyo, G. 2015. Characterization of the antifungal and plant growth-promoting effects of diffusible and volatile organic compounds produced by Pseudomonas fluorescens strains. Biol. Control 81:83-92.   DOI
5 Huang, X.-F., Chaparro, J. M., Reardon, K. F., Zhang, R., Shen, Q. and Vivanco, J. M. 2014. Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267-275.   DOI
6 Jacoby, R. P. and Kopriva, S. 2019. Metabolic niches in the rhizosphere microbiome: new tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange. J. Exp. Bot. 70:1087-1094.   DOI
7 Kim, D. R., Cho, G., Jeon, C. W., Weller, D. M., Thomashow, L. S., Paulitz, T. C. and Kwak, Y. S. 2019a. A mutualistic interaction between Streptomyces bacteria, strawberry plants and pollinating bees. Nat. Commun. 10:4802.
8 Kim, D.-R., Jeon, C.-W., Cho, G., Thomashow, L. S., Weller, D. M., Paik, M.-J., Lee, Y. B. and Kwak, Y.-S. 2021. Glutamic acid reshapes the plant microbiota to protect plants against pathogens. Microbiome 9:244.
9 Kloepper, J. W., Schroth, M. N. and Miller, T. D. 1980. Effects of rhizosphere colonization by plant growth-promoting rhizobacteria on potato plant development and yield. Phytopathology 70:1078-1082.   DOI
10 Schmalzer, S. 2016. Red revolution, green revolution: scientific farming in socialist China. The University of Chicago Press, Chicago, IL, USA. 320 pp.
11 Singh, B. K., Liu, H. and Trivedi, P. 2020. Eco-holobiont: a new concept to identify drivers of host-associated microorganisms. Environ. Microbiol. 22:564-567.   DOI
12 Singh, D. P., Gupta, V. K. and Prabha, R. 2019. Microbial interventions in agriculture and environment. Vol. 2. Rhizosphere, microbiome and agro-ecology. Springer, Singapore. 573 pp.
13 Berendsen, R. L., Vismans, G., Yu, K., Song, Y., de Jonge, R., Burgman, W. P., Burmolle, M., Herschend, J., Bakker, P. A. H. M. and Pieterse, C. M. J. 2018. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 12:1496-1507.   DOI
14 Brilli, F., Loreto, F. and Baccelli, I. 2019. Exploiting plant volatile organic compounds (VOCs) in agriculture to improve sustainable defense strategies and productivity of crops. Front. Plant Sci. 10:264.
15 Calvo, P., Nelson, L. and Kloepper, J. 2014. Agricultural uses of plant biostimulants. Plant Soil 383:3-41.   DOI
16 Bene, C., Barange, M., Subasinghe, R., Pinstrup-Andersen, P., Merino, G., Hemre, G.-I. and Williams, M. 2015. Feeding 9 billion by 2050 - putting fish back on the menu. Food Secur. 7:261-274.   DOI
17 Leclere, V., Bechet, M., Adam, A., Guez, J.-S., Wathelet, B., Ongena, M., Thonart, P., Gancel, F., Chollet-Imbert, M. and Jacques, P. 2005. Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism's antagonistic and biocontrol activities. Appl. Environ. Microbiol. 71:4577-4584.   DOI
18 Adejumo, T. O. and Orole, O. O. 2010. Effect of pH and moisture content on endophytic colonization of maize roots. Sci. Res. Essays 5:1655-1661.
19 Langridge, P. 2014. Reinventing the green revolution by harnessing crop mutant resources. Plant Physiol. 166:1682-1683.   DOI
20 Adair, K. L. and Douglas, A. E. 2017. Making a microbiome: the many determinants of host-associated microbial community composition. Curr. Opin. Microbiol. 35:23-29.   DOI
21 Araujo, R., Dunlap, C., Barnett, S. and Franco, C. M. M. 2019. Decoding wheat endosphere-rhizosphere microbiomes in Rhizoctonia solani-infested soils challenged by Streptomyces biocontrol agents. Front. Plant Sci. 10:1038.
22 Sparks, D. L. 2012. Advances in agronomy. Vol. 117. Academic Press, San Diego, CA, USA. 376 pp.
23 Thomashow, L. S. and Weller, D. M. 1988. Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici. J. Bacteriol. 170:3499-3508.   DOI
24 Turner, T. R., James, E. K. and Poole, P. S. 2013. The plant microbiome. Genome Biol. 14:209.
25 van der Heijden, M. G. and Hartmann, M. 2016. Networking in the plant microbiome. PLoS Biol. 14:e1002378.
26 Vannier, N., Agler, M. and Hacquard, S. 2019. Microbiota-mediated disease resistance in plants. PLoS Pathog. 15:e1007740.
27 Vargas-Hernandez, M., Macias-Bobadilla, I., Guevara-Gonzalez, R. G., Romero-Gomez, S. J., Rico-Garcia, E., Ocampo-Velazquez, R. V., Alvarez-Arquieta, L. L. and Torres-Pacheco, I. 2017. Plant hormesis management with biostimulants of biotic origin in agriculture. Front. Plant Sci. 8:1762.
28 Badri, D. V., Weir, T. L., van der Lelie, D. and Vivanco, J. M. 2009. Rhizosphere chemical dialogues: plant-microbe interactions. Curr. Opin. Biotechnol. 20:642-650.   DOI
29 Vurukonda, S. S. K. P., Giovanardi, D. and Stefani, E. 2018. Plant growth promoting and biocontrol activity of Streptomyces spp. as endophytes. Int. J. Mol. Sci. 19:952.
30 Badri, D. V. and Vivanco, J. M. 2009. Regulation and function of root exudates. Plant Cell Environ. 32:666-681.   DOI
31 Bakker, M. G., Manter, D. K., Sheflin, A. M., Weir, T. L. and Vivanco, J. M. 2012. Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil. 360:1-13.   DOI
32 Bakker, P., Pieterse, C., de Jonge, R. and Berendsen, R. L. 2018. The soil-borne legacy. Cell 172:1178-1180.   DOI
33 O'Banion, B. S., O'Neal, L., Alexandre, G. and Lebeis, S. L. 2020. Bridging the gap between single-strain and community-level plant-microbe chemical interactions. Mol. Plant-Microbe Interact. 33:124-134.   DOI
34 Berg, G., Rybakova, D., Grube, M. and Koberl, M. 2016. The plant microbiome explored: implications for experimental botany. J. Exp. Bot. 67:995-1002.   DOI
35 Backer, R., Rokem, J. S., Ilangumaran, G., Lamont, J., Praslickova, D., Ricci, E., Subramanian, S. and Smith, D. L. 2018. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front. Plant Sci. 9:1473.
36 Liu, H., Carvalhais, L. C., Crawford, M., Singh, E., Dennis, P. G., Pieterse, C. M. J. and Schenk, P. M. 2017. Inner plant values: diversity, colonization and benefits from endophytic bacteria. Front. Microbiol. 8:2552.
37 Rosenberg, E. and Zilber-Rosenberg, I. 2016. Microbes drive evolution of animals and plants: the hologenome concept. MBio 7:e01395.
38 Santoyo, G., del Carmen Orozco-Mosqueda, M. and Govindappa, M. 2012. Mechanisms of biocontrol and plant growthpromoting activity in soil bacterial species of Bacillus and Pseudomonas: a review. Biocontrol Sci. Technol. 22:855-872.   DOI
39 Liu, H. and Brettell, L. E. 2019. Plant defense by VOC-induced microbial priming. Trends Plant Sci. 24:187-189.   DOI
40 Zilber-Rosenberg, I. and Rosenberg, E. 2008. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32:723-735.   DOI
41 Liu, H., Macdonald, C. A., Cook, J., Anderson, I. C. and Singh, B. K. 2019. An ecological loop: host microbiomes across multitrophic interactions. Trends Ecol. Evol. 34:1118-1130.   DOI
42 Parakhia, M. V. and Golakiya, B. A. 2018. Manipulation of phytobiome: a new concept to control the plant disease and improve the productivity. J. Bacteriol. Mycol. 6:322-324.
43 Rodriguez, R. and Duran, P. 2020. Natural holobiome engineering by using native extreme microbiome to counteract the climate change effects. Front. Bioeng. Biotechnol. 8:568.
44 Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J. and Dowling, D. N. 2008. Bacterial endophytes: recent developments and applications. FEMS Microbiol. Lett. 278:1-9.   DOI
45 Saleem, M., Arshad, M., Hussain, S. and Bhatti, A. S. 2007. Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. J. Ind. Microbiol. Biotechnol. 34:635-648.   DOI
46 Santoyo, G., Hernandez-Pacheco, C., Hernandez-Salmeron, J. and Hernandez-Leon, R. 2017. The role of abiotic factors modulating the plant-microbe-soil interactions toward sustainable agriculture. a review. Span. J. Agric. Res. 15:e03R01.
47 Santoyo, G., Moreno-Hagelsieb, G., del Carmen OrozcoMosqueda, M. and Glick, B. R. 2016. Plant growth-promoting bacterial endophytes. Microbiol. Res. 183:92-99.   DOI
48 Colombo, E. M., Kunova, A., Pizzatti, C., Saracchi, M., Cortesi, P. and Pasquali, M. 2019. Selection of an endophytic Streptomyces sp. strain DEF09 from wheat roots as a biocontrol agent against Fusarium graminearum. Front. Microbiol. 10:2356.
49 Martinez-Absalon, S., Rojas-Solis, D., Hernandez-Leon, R., Prieto-Barajas, C., del Carmen Orozco-Mosqueda, M., PenaCabriales, J. J., Sakuda, S., Valencia-Cantero, E. and Santoyo, G. 2014. Potential use and mode of action of the new strain Bacillus thuringiensis UM96 for the biological control of the grey mould phytopathogen Botrytis cinerea. Biocontrol Sci. Technol. 24:1349-1362.   DOI
50 Chaparro, J. M., Sheflin, A. M., Manter, D. K. and Vivanco, J. M. 2012. Manipulating the soil microbiome to increase soil health and plant fertility. Biol. Fertil. Soils 48:489-499.   DOI
51 del Carmen Orozco-Mosqueda, M., del Carmen Rocha-Granados, M., Glick, B. R. and Santoyo, G. 2018. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol. Res. 208:25-31.   DOI
52 Du Jardin, P. 2015. Plant biostimulants: definition, concept, main categories and regulation. Sci. Hortic. 196:3-14.   DOI
53 Etesami, H. and Beattie, G. A. 2017. Plant-microbe interactions in adaptation of agricultural crops to abiotic stress conditions. In: Probiotics and plant health, eds. by V. Kumar, M. Kumar, S. Sharma and R. Prasad, pp. 163-200. Springer, Singapore.
54 Foley, J. A. 2011. Can we feed the world and sustain the planet? Sci. Am. 305:60-65.   DOI
55 Hamonts, K., Trivedi, P., Garg, A., Janitz, C., Grinyer, J., Holford, P., Botha, F. C., Anderson, I. C. and Singh, B. K. 2018. Field study reveals core plant microbiota and relative importance of their drivers. Environ. Microbiol. 20:124-140.   DOI
56 Dudareva, N., Klempien, A., Muhlemann, J. K. and Kaplan, I. 2013. Biosynthesis, function and metabolic engineering of plant volatile organic compounds. New Phytol. 198:16-32.   DOI
57 Haney, C. H., Samuel, B. S., Bush, J. and Ausubel, F. M. 2015. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat. Plants 1: 15051.
58 Compant, S., Duffy, B., Nowak, J., Clement, C. and Barka, E. A. 2005. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71:4951-4959.   DOI
59 Cha, J.-Y., Han, S., Hong, H.-J., Cho, H., Kim, D., Kwon, Y., Kwon, S.-K., Crusemann, M., Lee, Y. B., Kim, J. F., Giaever, G., Nislow, C., Moore, B. S., Thomashow, L. S., Weller, D. M. and Kwak, Y.-S. 2016. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 10:119-129.   DOI
60 Glick, B. R. 2012. Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:963401.
61 Harir, M., Bendif, H., Bellahcene, M., Fortas, Z. and Pogni, R. 2018. Streptomyces secondary metabolites. In: Basic biology and applications of Actinobacteria, ed. by S. Enany, pp. 99-122. IntechOpen, London, UK.
62 Huang, A. C., Jiang, T., Liu, Y.-X., Bai, Y.-C., Reed, J., Qu, B., Goossens, A., Nutzmann, H.-W., Bai, Y. and Osbourn, A. 2019. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364:eaau6389.
63 Kauffman, G. L., Kneivel, D. P. and Watschke, T. L. 2007. Effects of a biostimulant on the heat tolerance associated with photosynthetic capacity, membrane thermostability, and polyphenol production of perennial ryegrass. Crop Sci. 47:261-267.   DOI
64 Weller, D. M., Mavrodi, D. V., van Pelt, J. A., Pieterse, C. M. J., van Loon, L. C. and Bakker, P. A. H. M. 2012. Induced systemic resistance in Arabidopsis thaliana against Pseudomonas syringae pv. tomato by 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens. Phytopathology 102:403-412.   DOI
65 Kim, D.-R., Jeon, C.-W., Shin, J.-H., Weller, D. M., Thomashow, L. and Kwak, Y.-S. 2019b. Function and distribution of a lantipeptide in strawberry fusarium wilt disease-suppressive soils. Mol. Plant-Microbe Interact. 32:306-312.   DOI
66 Hassani, M. A., Duran, P. and Hacquard, S. 2018. Microbial interactions within the plant holobiont. Microbiome 6:158.
67 Yang, C.-Y., Ho, Y.-C., Pang, J.-C., Huang, S.-S. and Tschen, J. S.-M. 2009. Cloning and expression of an antifungal chitinase gene of a novel Bacillus subtilis isolate from Taiwan potato field. Bioresour. Technol. 100:1454-1458.   DOI
68 Worsley, S. F., Newitt, J., Rassbach, J., Batey, S., Holmes, N. A., Murrell, J. C., Wilkinson, B. and Hutchings, M. I. 2020. Streptomyces endophytes promote host health and enhance growth across plant species. Appl. Environ. Microbiol. 86:e01053-e01020.