1
Aamir M, Samal S, Rai A, Kashyap SP, Singh SK, Ahmed M, et al. Chapter 25 - Plant microbiome: diversity, distribution, and functional relevance in crop improvement and sustainable agriculture. In: White J, Kumar A, Droby S, editors., et al., Microbiome Stimulants for Crops. Woodhead Publishing; 2021. p. 417–36.
2
Orozco-Mosqueda MD, Rocha-Granados MD, Glick BR, Santoyo G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol Res. 2018;208:25–31.
https://doi.org/10.1016/j.micres.2018.01.005.
3
Lau, SE., Teo, W.F.A., Teoh, E.Y. et al. Microbiome engineering and plant biostimulants for sustainable crop improvement and mitigation of biotic and abiotic stresses. Discov Food 2, 9 (2022).
https://doi.org/10.1007/s44187-022-00009-5
5
Fincheira P, Quiroz A, Tortella G, Diez MC, Rubilar O. Current advances in plant-microbe communication via volatile organic compounds as an innovative strategy to improve plant growth. Microbiol Res. 2021;247:126726.
https://doi.org/10.1016/j.micres.2021.126726.
6
Ryu C-M, Farag MA, Hu C-H, Reddy MS, Wei H-X, Paré PW, et al. Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci USA. 2003;100(8):4927–32.
https://doi.org/10.1073/pnas.0730845100.
7
Jiang CH, Xie YS, Zhu K, Wang N, Li ZJ, Yu GJ, et al. Volatile organic compounds emitted by Bacillus sp JC03 promote plant growth through the action of auxin and strigolactone. Plant Growth Regul. 2019;87(2):317–28.
https://doi.org/10.1007/s10725-018-00473-z.
8
Rojas-Solís D, Zetter-Salmón E, Contreras-Pérez M, Rocha-Granados MC, Macías-Rodríguez L, Santoyo G. Pseudomonas stutzeri E25 and Stenotrophomonas maltophilia CR71 endophytes produce antifungal volatile organic compounds and exhibit additive plant growth-promoting effects. Biocatal Agric Biotechnol. 2018;13:46–52.
https://doi.org/10.1016/j.bcab.2017.11.007.
9
Vacheron J, Desbrosses G, Bouffaud M-L, Touraine B, Moënne-Loccoz Y, Muller D, et al. Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci. 2013;4:356.
https://doi.org/10.3389/fpls.2013.00356.
12
Wu L, Xiao W, Chen G, Song D, Khaskheli MA, Li P, et al. Identification of Pseudomonas mosselii BS011 gene clusters required for suppression of rice blast fungus Magnaporthe oryzae. J Biotechnol. 2018;282:1–9.
https://doi.org/10.1016/j.jbiotec.2018.04.016.
13
Turan M, Kıtır N, Alkaya Ü, Günes A, Tüfenkçi Ş, Yıldırım E, et al. Making Soil More Accessible to Plants: The Case of Plant Growth Promoting Rhizobacteria. In: Rigobelo EC, editor., et al., Plant Growth. New York: IntechOpen; 2016. p. 61–9.
15
Yoolong S, Kruasuwan W, Pham HTT, Jaemsaeng R, Jantasuriyarat C, Thamchaipenet A. Modulation of salt tolerance in Thai jasmine rice (Oryza sativa L cv KDML105) by Streptomyces venezuelae ATCC 10712 expressing ACC deaminase. Sci Rep. 2019;9(1):1275.
https://doi.org/10.1038/s41598-018-37987-5.
16
Gou W, Tian L, Ruan Z, Zheng P, Chen F, Zhang L, et al. Accumulation of choline and glycinebetaine and drought stress tolerance induced in maize (Zea mays) by three plant growth promoting rhizobacteria (PGPR) strains. Pak J Bot. 2015;47(2):581–6.
20
Basak A. Biostimulators–definitions, classification and legislation. In: Gawrońska H, editor. Monographs Series: Biostimulators in Modern Agriculture. General Aspects. Warsaw: Wieś Jutra; 2008. p. 7–17
21
Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH. Going back to the roots: The microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013;11(11):789–99.
https://doi.org/10.1038/nrmicro3109
22
Graham P.H., Vance C.P. Legumes: Importance and constraints to greater use. Plant Physiol. 2003;131:872–877. doi: 10.1104/pp.017004. [DOI] [PMC free article] [PubMed] [Google Scholar]
23
Rosenblueth M., Ormeño-Orrillo E., López-López A., Rogel M.A., Reyes-Hernández B.J., Martínez-Romero J.C., Reddy P.M., Martínez-Romero E. Nitrogen Fixation in Cereals. Front. Microbiol. 2018;9:9. doi: 10.3389/fmicb.2018.01794.
24
Morris J.J., Schniter E.J. Black Queen markets: Commensalism, dependency, and the evolution of cooperative specialization in human society. J. Bioecon. 2018;20:69–105. doi: 10.1007/s10818-017-9263-x.
25
S. Ali, J. Duan, T.C. Charles, B.R. Glick A bioinformatics approach to the determination of genes involved in endophytic behavior in Burkholderia spp J. Theor. Biol., 343 (2014), pp. 193-198
26
Schultze M., Kondorosi A.J. Regulation of symbiotic root nodule development. Annu. Rev. Genet. 1998;32:33–57. doi: 10.1146/annurev.genet.32.1.33.
27
Oldroyd G.E., Downie J.A. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu. Rev. Plant Biol. 2008;59:519–546. doi: 10.1146/annurev.arplant.59.032607.092839.
28
Desbrosses G.J., Stougaard J. Root nodulation: A paradigm for how plant-microbe symbiosis influences host developmental pathways. Cell Host Microbe. 2011;10:348–358. doi: 10.1016/j.chom.2011.09.005.
29
Yates M., Jones C. Advances in Microbial Physiology. Volume 11. Elsevier BV; Amsterdam, The Netherlands: 1974. Respiration and Nitrogen Fixation in Azotobacter; pp. 97–135.
30
Poole R.K., Hill S. Respiratory protection of nitrogenase activity in Azotobacter vinelandii—Roles of the terminal oxidases. Biosci. Rep. 1997;17:303–317.
31
Biswas B., Gresshoff P.M. The role of symbiotic nitrogen fixation in sustainable production of biofuels. Int. J. Mol. Sci. 2014;15:7380–7397.
32
Wopereis J., Pajuelo E., Dazzo F.B., Jiang Q., Gresshoff P.M., De Bruijn F.J., Stougaard J., Szczyglowski K. Short root mutant of Lotus japonicus with a dramatically altered symbiotic phenotype. Plant J. 2000;23:97–114.
33
Newcomb W., Sippell D., Peterson R.J. The early morphogenesis of Glycine max and Pisum sativum root nodules. Can. J. Bot. 1979;57:2603–2616.
34
Rolfe B.G., Gresshoff P.J., Biology P.M. Genetic analysis of legume nodule initiation. Annu. Rev. Plant Physiol. Plant Mol. Biol. 1988;39:297–319.
35
Zapata F., Danso S.K.A., Hardarson G., Fried M. Time Course of Nitrogen Fixation in Field-Grown Soybean Using Nitrogen-15 Methodology1. Agron. J. 1987;79:172–176.
36
A.O. Adesemoye, J.W. Kloepper Plant-microbes interactions in enhanced fertilizer-use efficiency Appl. Microbiol. Biotechnol., 85 (2009), pp. 1-12
37
G. Santoyo, G. Moreno-Hagelsieb, Ma del C. Orozco-Mosqueda, B.R. Glick Plant growth-promoting bacterial endophytes Microbiol. Res., 183 (2016), pp. 92-99
38
S. Ali, T.C. Charles, B.R. Glick Delay of flower senescence by bacterial endophytes expressing 1-aminocyclopropane-1-carboxylate deaminase J. Appl. Microbiol., 113 (2012), pp. 1139-1144
39
B.G. Coutinho, D. Licastro, L. Mendonça-Previato, M. Cámara, V. Venturi Plant-influenced gene expression in the rice endophyt: Burkholderia kururiensis M130 Mol. Plant Microbe Interact., 28 (2015), pp. 10-21
40
J.A. Vorholt Microbial life in the phyllosphere Nat. Rev. Microbiol., 10 (2012), p. 828
43
Yang WL, Gong T, Wang JW, Li GJ, Liu YY, Zhen J, et al. Effects of compound microbial fertilizer on soil characteristics and yield of wheat (Triticum aestivum L). Soil Sci Plant Nutr. 2020;20(4):2740–8.
https://doi.org/10.1007/s42729-020-00340-9.
45
Wang ZK, Chen ZY, Kowalchuk GA, Xu ZH, Fu XX, Kuramae EE. Succession of the resident soil microbial community in response to periodic inoculations. Appl Environ Microbiol. 2021;87(9):16.
https://doi.org/10.1128/aem.00046-21.
47
Rodriguez R, Duran P. Natural holobiome engineering by using native extreme microbiome to counteract the climate change effects. Front Bioeng Biotechnol. 2020;8:14.
https://doi.org/10.3389/fbioe.2020.00568.
48
Gou W, Tian L, Ruan Z, Zheng P, Chen F, Zhang L, et al. Accumulation of choline and glycinebetaine and drought stress tolerance induced in maize (Zea mays) by three plant growth promoting rhizobacteria (PGPR) strains. Pak J Bot. 2015;47(2):581–6.
49
Cordell, D.,White, S. (2014): Life’s bottleneck: sustaining the world’s phosphorus for a food secure future. Annu. Rev. Environ. Resour. 39, 161–188.
51
Whipps, J.M., Hand, P., Pink, D. and Bending, G.D. (2008). Phyllosphere microbiology with special reference to diversity and plant genotype. J. Appl. Microbiol. 105: 1744 –1755.
52
Dugald E. Reid, Brett J. Ferguson, Satomi Hayashi, Yu-Hsiang Lin, Peter M. Gresshoff., Molecular mechanisms controlling legume autoregulation of nodulation Annals of Botany, Volume 108, Issue 5, October 2011, Pages 789–795,
https://doi.org/10.1093/aob/mcr205
53
Freiberg, E. (1998) Microclimatic parameters influencing nitrogen fixation in the phyllosphere in a Costa Rican premontane rain forest. Oecologia 117, 9–18.
54
Murty, M.G. (1983) Nitrogen fixation (acetylene‐reduction) in the phyllosphere of some economically important plants. Plant Soil 73, 151–153.
55
Miyamoto, T., Kawahara, M. and Minamisawa, K. (2004) Novel endophytic nitrogen‐fixing clostridia from the grass Miscanthus sinensis as revealed by terminal restriction fragment length polymorphism analysis. Appl Environ Microbiol 70, 6580–6586.
56
Rangel, Lorena & Leveau, Johan. (2024). Applied microbiology of the phyllosphere. Applied Microbiology and Biotechnology. 108. 10.1007/s00253-024-13042-4.
57
Michael Fürnkranz, Wolfgang Wanek, Andreas Richter, Guy Abell, Frank Rasche & Angela Sessitsch., Nitrogen fixation by phyllosphere bacteria associated with higher plants and their colonizing epiphytes of a tropical lowland rainforest of Costa Rica The ISME Journal volume 2, pages561–570 (2008)
58
Aasfar A, Bargaz A, Yaakoubi K, Hilali A, Bennis I, Zeroual Y and Meftah Kadmiri I (2021) Nitrogen Fixing Azotobacter Species as Potential Soil Biological Enhancers for Crop Nutrition and Yield Stability. Front. Microbiol. 12:628379. doi: 10.3389/fmicb.2021.628379
59
Levicán, G., Ugalde, J.A., Ehrenfeld, N. et al. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9, 581 (2008).
https://doi.org/10.1186/1471-2164-9-581