Yang, J., Kloepper, J. W. & Ryu, C. M. Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci. 14, 1–4 (2009).
Kearl, J. et al. Salt-tolerant halophyte rhizosphere bacteria stimulate growth of alfalfa in salty soil. Front. Microbiol. 10, 1849. https://doi.org/10.3389/fmicb.2019.01849 (2019).
Khan, N. et al. Comparative physiological and metabolic analysis reveals a complex mechanism involved in drought tolerance in Chickpea (Cicer arietinum L.) induced by PGPR and PGRs. Sci. Rep. 9, 2097. https://doi.org/10.1038/s41598-019-38702-8 (2019).
Compant, S., Samad, A., Faist, H. & Sessitsch, A. A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. J. Adv. Res. 19, 29–37 (2019).
Bruto, M., Prigent-Combaret, C., Muller, D. & Moënne-Loccoz, Y. Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Sci. Rep. 4, 6261. https://doi.org/10.1038/srep06261 (2014).
Timmusk, S. Perspectives and challenges of microbial application for crop improvement. Front. Plant Sci. 8, 49. https://doi.org/10.3389/fpls.2017.00049 (2017).
Sessitsch, A., Pfaffenbichler, N. & Mitter, B. Microbiome applications from lab to field: facing complexity. Trends Plant Sci. 24, 194–198 (2019).
Olanrewaju, O. S., Glick, B. R. & Babalola, O. O. Mechanisms of action of plant growth promoting bacteria. World J. Microb. Biot 33, 197. https://doi.org/10.1007/s11274-017-2364-9 (2017).
Gupta, A. et al. Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PLoS ONE 9, e104259. https://doi.org/10.1371/journal.pone.0104259 (2014).
Pérez-Jaramillo, J. E., Carrión, V. J., de Hollander, M. & Raaijmakers, J. M. The wild side of plant microbiomes. Microbiome 6, 143. https://doi.org/10.1186/s40168-018-0519-z (2018).
Song, J. Y. et al. Genome sequence of the Plant Growth-Promoting Rhizobacterium Bacillus sp. strain JS. J. Bacteriol. 19, 14. https://doi.org/10.1128/JB.00676-12 (2012).
Duan, J., Jiang, W., Cheng, Z., Heikkila, J. J. & Glick, B. R. The complete genome sequence of the Plant Growth-Promoting bacterium Pseudomonas sp. UW4. PLoS ONE 8, e58640. https://doi.org/10.1371/journal.pone.0058640 (2013).
Li, S. et al. Complete genome sequence of Paenibacillus polymyxa SQR-21, a plant growth-promoting rhizobacterium with antifungal activity and rhizosphere colonization ability. Genome Announc. 2, e00281-e314. https://doi.org/10.1128/genomeA.00281-14 (2014).
Fierer, N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Rev. Microbiol. 15, 579–590 (2017).
Penrose, D. M. & Glick, B. R. Methods for isolating and characterizing ACC deaminase-containing plant growth-promoting rhizobacteria. Physiol. Plantarum 118, 10–15 (2003).
Lo, K. J., Lin, S. S., Lu, C. W., Kuo, C. H. & Liu, C. T. Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3). Sci. Rep. 8, 12769. https://doi.org/10.1038/s41598-018-31128-8 (2018).
Liu, W. et al. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A. Sci. Rep. 6, 20–22 (2016).
Andrés-Barrao, C. et al. Complete genome sequence analysis of Enterobacter sp. SA187, a plant multi-stress tolerance promoting endophytic bacterium. Front. Microbiol. 8, 2023. https://doi.org/10.3389/fmicb.2017.02023 (2017).
Esmaeel, Q. et al. Draft genome sequence of plant growth-promoting Burkholderia sp. strain BE12, isolated from the rhizosphere of maize. Genome Announc. 6, e00299-18. https://doi.org/10.1128/genomeA.00299-18 (2018).
Wang, Z. et al. Draft genome analysis offers insights into the mechanism by which Streptomyces chartreusis WZS021 increases drought tolerance in sugarcane. Front. Microbiol. 10, 3262. https://doi.org/10.3389/fmicb.2018.03262 (2019).
Matteoli, F. P. et al. Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost. BMC Genomics 19, 750. https://doi.org/10.1186/s12864-018-5130-y (2018).
Yu, Z. et al. Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T. Stand. Genomic Sci. 13, 28. https://doi.org/10.1186/s40793-018-0322-2 (2018).
Westerman, R. L. Soil Testing and Plant Analysis. SSSA Book Series 3 3rd edn. (Madison, SSSA, 1990).
Bharti, N., Pandey, S. S., Barnawal, D., Patel, V. K. & Kalra, A. Plant growth promoting rhizobacteria Dietzia natronolimnaea modulates the expression of stress responsive genes providing protection of wheat from salinity stress. Sci. Rep. 6, 34768. https://doi.org/10.1038/srep34768 (2016).
Sharma, S., Kulkarni, J. & Jha, B. Halotolerant rhizobacteria promote growth and enhance salinity tolerance in peanut. Front. Microbiol. 7, 1600. https://doi.org/10.3389/fmicb.2016.01600 (2016).
Gupta, S. & Pandey, S. ACC Deaminase producing bacteria with multifarious plant growth promoting traits alleviates salinity stress in French Bean (Phaseolus vulgaris) plants. Front. Microbiol. 10, 1506. https://doi.org/10.3389/fmicb.2019.01506 (2019).
Pan, J. et al. The growth promotion of two salt-tolerant plant groups with PGPR inoculation: a meta-analysis. Sustainability 11, 378. https://doi.org/10.3390/su11020378 (2019).
Vurukonda, S. S. K. P., Vardharajula, S., Shrivastava, M. & SkZ, A. Multifunctional Pseudomonas putida strain FBKV2 from arid rhizosphere soil and its growth promotional effects on maize under drought stress. Rhizosphere 1, 4–13 (2016).
Marasco, R. et al. Salicornia strobilacea (synonym of Halocnemum strobilaceum) grown under different tidal regimes selects rhizosphere bacteria capable of promoting plant growth. Front. Microbiol. 7, 1286. https://doi.org/10.3389/fmicb.2016.01286 (2016).
Mukhtar, S. et al. Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome. World J. Microb. Biot. 34, 136. https://doi.org/10.1007/s11274-018-2509-5 (2018).
Patten, C. L. & Glick, B. R. Role of Pseudomonas putida indoleacetic acid in development of the host plant root system Appl. Environ. Microbiol. 68(3795), 3801 (2002).
Etesami, H., Alikhani, H. A. & Hosseini, H. M. Indole-3-acetic acid (IAA) production trait, a useful screening to select endophytic and rhizosphere competent bacteria for rice growth promoting agents. MethodsX 2, 72–78 (2015).
Abbamondi, G. R. et al. Plant growth-promoting effects of rhizospheric and endophytic bacteria associated with different tomato cultivars and new tomato hybrids. Chem. Biol. Technol. Agric. 3, 1. https://doi.org/10.1186/s40538-015-0051-3 (2016).
Gupta, S. & Pandey, S. Unravelling the biochemistry and genetics of ACC deaminase-An enzyme alleviating the biotic and abiotic stress in plants. Plant gene 18, 100175. https://doi.org/10.1016/j.plgene.2019.100175 (2019).
Khamna, S., Yokota, A., Peberdy, J. F. & Lumyong, S. Indole-3-acetic acid production by Streptomyces sp. isolated from some Thai medicinal plant rhizosphere soils. EurAsian J. BioSciences 4, 23–32 (2010).
Spaepen, S. & Vanderleyden, J. Auxin and plant-microbe interactions. C. S. H. Perspect. Biol. 3, a001438. https://doi.org/10.1101/cshperspect.a001438 (2011).
Patten, C. L. & Glick, B. R. Bacterial biosynthesis of indole-3-acetic acid. Can. J. Microbiol. 42, 207–220 (1996).
Majeed, A., Abbasi, K. M., Hameed, S., Imran, A. & Rahim, N. Isolation and characterization of plant growth-promoting rhizobacteria from wheat rhizosphere and their effect on plant growth promotion. Front. Microbiol. 6, 198. https://doi.org/10.3389/fmicb.2015.00198 (2015).
Apine, O. A. & Jadhav, J. P. Optimization of medium for indole-3-acetic acid production using Pantoea agglomerans strain PVM. J. Appl. Microbiol. 110, 1235–1244 (2011).
Checcucci, A. et al. Role and regulation of ACC deaminase gene in Sinorhizobium melilotr: Is it a symbiotic, rhizospheric or endophytic gene?. Front. Genet. 8, 6. https://doi.org/10.3389/fgene.2017.00006 (2017).
Belimov, A. A. et al. Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.). Soil Biol. Biochem. 37, 241–250 (2005).
Khan, N. A., Khan, M. I. R., Ferrante, A. & Poor, P. Editorial: ethylene: a key regulatory molecule in plants. Front. Plant Sci. 8, 1782. https://doi.org/10.3389/fpls.2017.01782 (2017).
Glick, B. R. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol. Res. 169, 30–39 (2014).
Wang, Z. et al. Isolation and characterization of a phosphorus-solubilizing bacterium from rhizosphere soils and its colonization of Chinese Cabbage (Brassica campestris ssp. chinensis). Front. Microbiol. 8, 1270. https://doi.org/10.3389/fmicb.2017.01270 (2017).
Dinesh, R. et al. Isolation, characterization, and evaluation of multi-trait plant growth promoting rhizobacteria for their growth promoting and disease suppressing effects on ginger. Microbiol. Res. 173, 34–43 (2015).
Niu, X., Song, L., Xiao, Y. & Ge, W. Drought-tolerant plant growth-promoting rhizobacteria associated with foxtail millet in a semi-arid agroecosystem and their potential in alleviating drought stress. Front. Microbiol. 8, 2580. https://doi.org/10.3389/fmicb.2017.02580 (2018).
Singh, V. K., Singh, A. K., Singh, P. P. & Kumar, A. Interaction of plant growth promoting bacteria with tomato under abiotic stress: a review. Agricult. Ecosyst. Environ. 267, 129–140 (2018).
Grover, M., Bodhankar, S., Maheswari, M. & Srinivasarao, C. Actinomycetes as mitigators of climate change and abiotic stress. In Plant Growth Promoting Actinobacteria: A New Avenue for Enhancing the Productivity and Soil Fertility of Grain Legumes (eds Subramaniam, G. et al.) 203–212 (Springer, Berlin, 2016).
Sang, M. K., Jeong, J. J., Kim, J. & Kim, K. D. Growth promotion and root colonisation in pepper plants by phosphate-solubilising Chryseobacterium sp strain ISE14 that suppresses Phytophthora blight. Ann. Appl. Biol. 172, 208–223 (2018).
Xiao, X., Fan, M., Wang, E., Chen, W. & Wei, G. Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants. Appl. Microbiol. Biot. 101, 8485–8497 (2017).
Abdelkrim, S. et al. Effect of Pb-resistant plant growth-promoting rhizobacteria inoculation on growth and lead uptake by Lathyrus sativus. J. Basic Microb. 58, 579–589 (2018).
Liu, Y. et al. Characterization of Lysobacter capsici strain NF87–2 and its biocontrol activities against phytopathogens. Eur. J. Plant Pathol. 155, 859–869 (2019).
Edgar, R. C. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ. https://doi.org/10.7717/peerj.4652 (2018).
Lee, Z. M., Bussema, C. III. & Schmidt, T. M. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. 37, D489–D493 (2008).
Shen, X., Hu, H., Peng, H., Wang, W. & Zhang, X. Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics 14, 271. https://doi.org/10.1186/1471-2164-14-271 (2013).
Niazi, A. et al. Genome analysis of Bacillus amyloliquefaciens subsp. Plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management. PloS ONE 9, e104651. https://doi.org/10.1371/journal.pone.0104651 (2014).
Riggs, P. J., Chelius, M. K., Leonardo, I. A., Kaeppler, S. M. & Triplett, E. W. Enhanced maize productivity by inoculation with diazotrophic bacteria. Funct. Plant Biol. 28, 829–836 (2001).
Saleem, M., Arshad, M., Hussain, S. & Bhatti, A. S. Perspective of plant growth promoting rhizobacteria (PGPR) containing ACC deaminase in stress agriculture. J. Ind. Microbiol. Biot. 34, 635–648 (2007).
Dorjey, S., Gupta, V. & Razdan, V. K. Evaluation of Pseudomonas fluorescens isolates for the management of Fusarium oxysporum f.sp. lycopersici and Rhizoctonia solani causing wilt complex in tomato. Indian Phytopathol. 70, 127–130 (2017).
Dardanelli, M. S. et al. Changes in flavonoids secreted by Phaseolus vulgaris roots in the presence of salt and the plant growth-promoting rhizobacterium Chryseobacterium balustinum. Appl. Soil Ecol. 75, 31–38 (2012).
Ogut, M., Er, F. & Brohi, A. Excessive phosphorus fertilization does not increase cadmium concentrations in soil or carrots (Daucus carota L.) grown in Konya (Turkey). Acta Agr. Scand B-S.P. 60, 420–426 (2010).
Rodríguez, H., Fraga, R., Gonzalez, T. & Bashan, Y. Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil 287, 15–21 (2006).
Kalayu, G. Phosphate solubilizing microorganisms: Promising approach as biofertilizers. Int. J. Agron. 2019, 4917256. https://doi.org/10.1155/2019/4917256 (2019).
Mellidou, I. et al. Silencing S-adenosyl-L-methionine decarboxylase (SAMDC) in Nicotiana tabacum points at a polyamine-dependent trade-off between growth and tolerance responses. Front. Plant Sci. 7, 379. https://doi.org/10.3389/fpls.2016.00379 (2016).
Michael, A. J. Biosynthesis of polyamines and polyamine-containing molecules. Biochem. J. 473, 2315–2329 (2016).
Nascimento, F. X., Hernández, A. G., Glick, B. R. & Rossi, M. J. Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. Biotechnol. Rep. 25, e00406. https://doi.org/10.1016/j.btre.2019.e00406 (2020).
Goswami, R. et al. Optimization of growth determinants of a potent cellulolytic bacterium isolated from lignocellulosic biomass for enhancing biogas production. Clean Technol. Envir. 18, 1565–1583 (2016).
Vokou, D., Giannakou, U., Kontaxi, C. & Vareltzidou, S. Axios. Aliakmon and gallikos delta complex, Νorthern Greece. In Encyclopedia of Wetlands, Vol. 4 World Wetlands (eds Finlayson, M. et al.) (Springer, Berlin, 2016).
Mellidou, I., Keulemans, J., Kanellis, A. & Davey, M. W. Regulation of fruit ascorbic acid concentrations in high and low vitamin C tomato cultivars during ripening. BMC Plant Biol. 12, 239–258 (2012).
Bouyoucos, G. J. Hydrometer method improved for making particle size analysis of soils. Agron. J. 54, 464–465 (1962).
Sparks, D. L. Methods of Soil Analysis – Part 3 – Chemical Methods, SSSA Book Series 5 (ASA. Madison, WI, SSSA, 1996).
Karamanoli, K., Bouligaraki, P., Constantinidou, H. I. & Lindow, S. E. Polyphenolic compounds on leaves limit iron availability and affect growth of epiphytic bacteria. Ann. Appl. Biol. 159, 99–108 (2011).
Eevers, N. et al. Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media. Microb. Biotechnol. 8, 707–715 (2015).
Louden, B. C., Haarmann, D. & Lynne, A. M. Use of blue agar CAS assay for siderophore detection. J. Microbiol. Biol. Educ. 12, 51. https://doi.org/10.1128/jmbe.v12i1.249 (2011).
García, C. A., De Rossi, B. P., Alcaraz, E., Vay, C. & Franco, M. Siderophores of Stenotrophomonas maltophilia: detection and determination of their chemical nature. Rev. Argent. Microbiol. 44, 150–154 (2012).
Dworkin, M. & Foster, J. Experiments with some microorganisms which utilize ethane and hydrogen. J. Bacteriol. 75, 592–601 (1958).
Hontzeas, N., Zoidakis, J., Glick, B. R. & Abu-Omar, M. M. Expression and characterization of 1-aminocyclopropane-1-carboxylate deaminase from the rhizobacterium Pseudomonas putida UW4: a key enzyme in bacterial plant growth promotion. Biochim. Biophys. Acta 1703, 11–19 (2004).
Bradford, M. A rapid and sensitive method for the quantitation of micro gram quantities of protein utilizing the principle of protein—dye binding. Anal. Biochem. 72, 248–258 (1976).
Nautiyal, C. S. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol. Lett. 170, 265–270 (1999).
Luziatelli, F., Ficca, A. G., Colla, G., Švecová, E. B. & Ruzzi, M. Foliar application of vegetal-derived bioactive compounds stimulates the growth of beneficial bacteria and enhances microbiome biodiversity in lettuce. Front. Plant Sci. 10, 60. https://doi.org/10.3389/fpls.2019.00060 (2019).
Herlemann, D. P. R. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2, W537–W544 (2018).
Li, D. et al. MEGAHIT v.10: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 1, 3–11 (2016).
Seeman, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 15, 2068–2069 (2014).
Thompson, J. D., Gibson, T. J. & Higgins, D. G. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinform. https://doi.org/10.1002/0471250953.bi0203s00 (2002).
Hall, T. A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acid S. 41, 95–98 (1999).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Felsenstein, J. Confidence limits on phylogenies: an approach using the Bootstrap. Evolution 39, 783–791 (1985).
Wu, S., Zhu, Z., Fu, L., Niu, B. & Li, W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12, 444. https://doi.org/10.1186/1471-2164-12-444 (2011).
Kamou, N. N. et al. Isolation screening and characterisation of local beneficial rhizobacteria based upon their ability to suppress the growth of Fusarium oxysporum f. sp. radicis-lycopersici and tomato foot and root rot. Biocontrol Sci. Technol. 25(8), 928–949 (2015).
Source: Ecology - nature.com
