Adeleke B.S., Babalola O.O. (2020): The endosphere microbial communities, a great promise in agriculture. International Microbiology, 24: 1–17.
https://doi.org/10.1007/s10123-020-00140-2
Adeleke B.S., Ayangbenro A.S., Babalola O.O. (2021): Genomic assessment of Stenotrophomonas indicatrix for improved sunflower plant. Current Genetics, 67: 891–907.
https://doi.org/10.1007/s00294-021-01199-8
Alexander A., Singh V.K., Mishra A., Jha B. (2019): Plant growth-promoting rhizobacterium Stenotrophomonas maltophilia BJ01 augments endurance against N2 starvation by modulating physiology and biochemical activities of Arachis hypogea. PLoS One, 14: e0222405. doi: 10.1371/journal.pone.0222405
https://doi.org/10.1371/journal.pone.0222405
Alkahtani M.D., Fouda A., Attia K.A., Al-Otaibi F., Eid A.M., Ewais E.E.D., Hijri M., St-Arnaud M., Hassan S.E.D., Khan N. (2020): Isolation and characterization of plant growth-promoting endophytic bacteria from desert plants and their application as bioinoculants for sustainable agriculture. Agronomy, 10: 1325. doi: 10.3390/agronomy10091325
https://doi.org/10.3390/agronomy10091325
Arkin A.P., Cottingham R.W., Henry C.S., Harris N.L., Stevens R.L., Maslov S., Dehal P., Ware D., Perez F., Canon S. (2018): KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36: 566–569.
https://doi.org/10.1038/nbt.4163
Bashir S., Iqbal A., Hasnain S. (2020): Comparative analysis of endophytic bacterial diversity between two varieties of sunflower Helianthus annuus with their PGP evaluation. Saudi Journal of Biological Sciences, 27: 720–726.
https://doi.org/10.1016/j.sjbs.2019.12.010
Battu L., Ulaganathan K. (2020): Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. KU-LS. Functional and Integrative Genomics, 20: 237–243.
https://doi.org/10.1007/s10142-019-00713-z
Babraham Bioinformatics (2011): FastQC: A quality control tool for high throughput sequence data. Cambridge, Babraham Institute. Available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Bolger A.M., Lohse M., Usadel B. (2014): Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30: 2114–2120.
https://doi.org/10.1093/bioinformatics/btu170
Cavalcanti M.I.P., de Carvalho Nascimento R., Rodrigues D.R., Escobar I.E.C., Fraiz A.C.R., de Souza A.P., de Freitas A.D.S., Nóbrega R.S.A., Fernandes-Júnior P.I. (2020): Maize growth and yield promoting endophytes isolated into a legume root nodule by a cross-over approach. Rhizosphere, 15: 100211. doi: 10.1016/j.rhisph.2020.100211
https://doi.org/10.1016/j.rhisph.2020.100211
Cimermancic P., Medema M.H., Claesen J., Kurita K., Brown L.C.W., Mavrommatis K., Pati A., Godfrey P.A., Koehrsen M., Clardy J. (2014): Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell, 158: 412–421.
https://doi.org/10.1016/j.cell.2014.06.034
Egamberdieva D., Jabborova D., Berg G. (2016): Synergistic interactions between Bradyrhizobium japonicum and the endophyte Stenotrophomonas rhizophila and their effects on growth, and nodulation of soybean under salt stress. Plant and Soil, 405: 35–45.
https://doi.org/10.1007/s11104-015-2661-8
Egamberdieva D., Alimov J., Shurigin V., Alaylar B., Wirth S., Bellingrath-Kimura S.D. (2022): Diversity and plant growth-promoting ability of endophytic, halotolerant bacteria associated with Tetragonia tetragonioides (Pall.) Kuntze. Plants, 11: 49. doi: 10.3390/plants11010049
https://doi.org/10.3390/plants11010049
Etesami H., Alikhani H.A. (2016): Suppression of the fungal pathogen Magnaporthe grisea by Stenotrophomonas maltophilia, a seed-borne rice (Oryza sativa L.) endophytic bacterium. Archives of Agronomy and Soil Science, 62: 1271–1284.
https://doi.org/10.1080/03650340.2016.1139087
Fadiji A.E., Babalola O.O. (2020): Exploring the potentialities of beneficial endophytes for improved plant growth. Saudi Journal of Biological Sciences, 27: 3622–3633.
https://doi.org/10.1016/j.sjbs.2020.08.002
Fouda A., Eid A.M., Elsaied A., El-Belely E.F., Barghoth M.G., Azab E., Gobouri A.A., Hassan S.E.D. (2021): Plant growth-promoting endophytic bacterial community inhabiting the leaves of Pulicaria incisa (Lam.) DC Inherent to arid regions. Plants, 10: 76. doi: 10.3390/plants10010076
https://doi.org/10.3390/plants10010076
Guerrieri M.C., Fiorini A., Fanfoni E., Tabaglio V., Cocconcelli P.S., Trevisan M., Puglisi E. (2021): Integrated genomic and greenhouse assessment of a novel plant growth-promoting rhizobacterium for tomato plant. Frontiers in Plant Science, 12: 660620. doi: 10.3389/fpls.2021.660620
https://doi.org/10.3389/fpls.2021.660620
Guo D.J., Singh R.K., Singh P., Li D.P., Sharma A., Xing Y.X., Song X.P., Yang L.T., Li Y.R. (2020): Complete genome sequence of Enterobacter roggenkampii ED5, a nitrogen fixing plant growth promoting endophytic bacterium with biocontrol and stress tolerance properties, isolated from sugarcane root. Frontiers in Microbiology, 11: 2270. doi: 10.3389/fmicb.2020.580081
https://doi.org/10.3389/fmicb.2020.580081
Gupta A., Gopal M., Thomas G.V., Manikandan V., Gajewski J., Thomas G., Seshagiri S., Schuster S.C., Rajesh P., Gupta R. (2014): 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. doi: 10.1371/journal.pone.0104259.t005
Gutierrez C.K., Matsui G.Y., Lincoln D.E., Lovell C.R. (2009): Production of the phytohormone indole-3-acetic acid by estuarine species of the genus Vibrio. Applied and Environmental Microbiology, 75: 2253–2258.
https://doi.org/10.1128/AEM.02072-08
Haidar B., Ferdous M., Fatema B., Ferdous A.S., Islam M.R., Khan H. (2018): Population diversity of bacterial endophytes from jute (Corchorus olitorius) and evaluation of their potential role as bioinoculants. Microbiological Research, 208: 43–53.
https://doi.org/10.1016/j.micres.2018.01.008
Hubrich F., Müller M., Andexer J.N. (2021): Chorismate-and isochorismate converting enzymes: Versatile catalysts acting on an important metabolic node. Chemical Communications, 57: 2441–2463.
https://doi.org/10.1039/D0CC08078K
Huelsenbeck J.P., Ronquist F. (2001): MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754–755.
https://doi.org/10.1093/bioinformatics/17.8.754
Igiehon N.O., Babalola O.O., Aremu B.R. (2019): Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress. BMC Microbiology, 19: 159. doi: 10.1186/s12866-019-1536-1
https://doi.org/10.1186/s12866-019-1536-1
Kang S.M., Asaf S., Khan A.L., Khan A., Mun B.G., Khan M.A., Gul H., Lee I.J. (2020): Complete genome sequence of Pseudomonas psychrotolerans CS51, a plant growth-promoting bacterium, under heavy metal stress conditions. Microorganisms, 8: 382. doi: 10.3390/microorganisms8030382
https://doi.org/10.3390/microorganisms8030382
Kasim W.A., Osman M.E., Omar M.N., Salama S. (2021): Enhancement of drought tolerance in Triticum aestivum L. seedlings using Azospirillum brasilense NO40 and Stenotrophomonas maltophilia B11. Bulletin of the National Research Centre, 45: 95. doi: 10.1186/s42269-021-00546-6
https://doi.org/10.1186/s42269-021-00546-6
Khalil A.M.A., Hassan S.E.D., Alsharif S.M., Eid A.M., Ewais E.E.D., Azab E., Gobouri A.A., Elkelish A., Fouda A. (2021): Isolation and characterization of fungal endophytes isolated from medicinal plant Ephedra pachyclada as plant growth-promoting. Biomolecules, 11: 140. doi: 10.3390/biom11020140
https://doi.org/10.3390/biom11020140
Khamwan S., Boonlue S., Riddech N., Jogloy S., Mongkolthanaruk W. (2018): Characterization of endophytic bacteria and their response to plant growth promotion in Helianthus tuberosus L. Biocatalysis and Agricultural Biotechnology, 13: 153–159.
https://doi.org/10.1016/j.bcab.2017.12.007
Khan M.S., Gao J., Zhang M., Chen X., Du Y., Yang F., Xue J., Zhang X. (2020): Isolation and characterization of plant growth-promoting endophytic bacteria Bacillus stratosphericus LW-03 from Lilium wardii. 3 Biotech, 10: 305. doi: 10.1007/s13205-020-02294-2
https://doi.org/10.1007/s13205-020-02294-2
Li R., Feng Y., Chen H., Zhang C., Huang Y., Chen L., Hao Q., Cao D., Yuan S., Zhou X. (2020): Whole-genome sequencing of Bradyrhizobium diazoefficiens 113-2 and comparative genomic analysis provide molecular insights into species specificity and host specificity. Frontiers in Microbiology, 11: 576800. doi: 10.3389/fmicb.2020.576800
https://doi.org/10.3389/fmicb.2020.576800
Liaquat F., Munis M.F.H., Arif S., Haroon U., Shengquan C., Qunlu L. (2020): Cd-tolerant SY-2 strain of Stenotrophomonas maltophilia: A potential PGPR, isolated from the Nanjing mining area in China. 3 Biotech, 10: 519. doi: 10.1007/s13205-020-02524-7
https://doi.org/10.1007/s13205-020-02524-7
Liu W., Wang Q., Hou J., Tu C., Luo Y., Christie P. (2016): Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A. Scientific Reports, 6: 26710. doi: 10.1038/srep26710
https://doi.org/10.1038/srep26710
Majeed A., Abbasi M.K., Hameed S., Imran A., Rahim N. (2015): Isolation and characterization of plant growth-promoting rhizobacteria from wheat rhizosphere and their effect on plant growth promotion. Frontiers in Microbiology, 6: 198. doi: 10.3389%2Ffmicb.2015.00198
https://doi.org/10.3389/fmicb.2015.00198
Nascimento F.X., Hernández A.G., Glick B.R., Rossi M.J. (2020a): Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest. Biotechnology Reports, 25: 406. doi: 10.1016/j.btre.2019.e00406
https://doi.org/10.1016/j.btre.2019.e00406
Nascimento F.X., Hernandez A.G., Glick B.R., Rossi M.J. (2020b): The extreme plant-growth-promoting properties of Pantoea phytobeneficialis MSR2 revealed by functional and genomic analysis. Environmental Microbiology, 22: 1341–1355.
https://doi.org/10.1111/1462-2920.14946
Nurk S., Bankevich A., Antipov D., Gurevich A.A., Korobeynikov A., Lapidus A., Prjibelski A.D., Pyshkin A., Sirotkin A., Sirotkin Y. (2013): Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology, 20: 714–737.
https://doi.org/10.1089/cmb.2013.0084
Nwachukwu B.C., Ayangbenro A.S., Babalola O.O. (2021): Comparative study of microbial structure and functional profle of sunfower rhizosphere grown in two felds. BMC Microbiology, 21: 337. doi: 10.1186/s12866-021-02397-7
https://doi.org/10.1186/s12866-021-02397-7
Oliverio A.M., Bissett A., McGuire K., Saltonstall K., Turner B.L., Fierer N. (2020): The role of phosphorus limitation in shaping soil bacterial communities and their metabolic capabilities. Mbio, 11: e01718. doi: 10.1128/mBio.01718-20
https://doi.org/10.1128/mBio.01718-20
Passari A.K., Chandra P., Mishra V.K., Leo V.V., Gupta V.K., Kumar B., Singh B.P. (2016): Detection of biosynthetic gene and phytohormone production by endophytic actinobacteria associated with Solanum lycopersicum and their plant-growth-promoting effect. Research in Microbiology, 167: 692–705.
https://doi.org/10.1016/j.resmic.2016.07.001
Pinski A., Zur J., Hasterok R., Hupert-Kocurek K. (2020): Comparative genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila revealed characteristic features of both species. International Journal of Molecular Sciences, 21: 4922. doi: 10.3390%2Fijms21144922
https://doi.org/10.3390/ijms21144922
Rahman M.D.M., Flory E., Koyro H.W., Abideen Z., Schikora A., Suarez C., Schnell S., Cardinale M. (2018): Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.). Systematic and Applied Microbiology, 41: 386–398.
https://doi.org/10.1016/j.syapm.2018.02.003
Rojas-Solís D., Zetter-Salmón E., Contreras-Pérez M., del Carmen Rocha-Granados M., Macías-Rodríguez L., Santoyo G. (2018): Pseudomonas stutzeri E25 and Stenotrophomonas maltophilia CR71 endophytes produce antifungal volatile organic compounds and exhibit additive plant growth-promoting effects. Biocatalysis and Agricultural Biotechnology, 13: 46–52.
https://doi.org/10.1016/j.bcab.2017.11.007
Samaras A., Nikolaidis M., Antequera-Gómez M.L., Cámara-Almirón J., Romero D., Moschakis T., Amoutzias G.D., Karaoglanidis G.S. (2020): Whole genome sequencing and root colonization studies reveal novel insights in the biocontrol potential and growth promotion by Bacillus subtilis MBI 600 on cucumber. Frontiers in Microbiology, 11: 600393. doi: 10.3389/fmicb.2020.600393
https://doi.org/10.3389/fmicb.2020.600393
Shastry R.P., Welch M., Rai V.R., Ghate S.D., Sandeep K., Rekha P. (2020): The whole-genome sequence analysis of Enterobacter cloacae strain Ghats1: Insights into endophytic lifestyle-associated genomic adaptations. Archives of Microbiology, 202: 1571–1579.
https://doi.org/10.1007/s00203-020-01848-5
Singh R.K., Singh P., Li H.B., Guo D.J., Song Q.Q., Yang L.T., Malviya M.K., Song X.P., Li Y.R. (2020): Plant-PGPR interaction study of plant growth-promoting diazotrophs Kosakonia radicincitans BA1 and Stenotrophomonas maltophilia COA2 to enhance growth and stress-related gene expression in Saccharum spp. Journal of Plant Interactions, 15: 427–445.
https://doi.org/10.1080/17429145.2020.1857857
Singh P., Singh R.K., Guo D.J., Sharma A., Singh R.N., Li D.P., Malviya M.K., Song X.P., Lakshmanan P., Yang L.T. (2021): Whole genome analysis of sugarcane root-associated endophyte Pseudomonas aeruginosa B18 – A plant growth-promoting bacterium with antagonistic potential against Sporisorium scitamineum. Frontiers in Microbiology, 12: 104. doi: 10.3389/fmicb.2021.628376
https://doi.org/10.3389/fmicb.2021.628376
Ulrich K., Kube M., Becker R., Schneck V., Ulrich A. (2021): Genomic analysis of the endophytic Stenotrophomonas strain 169 reveals features related to plant-growth promotion and stress tolerance. Frontiers in Microbiology, 12: 1542. doi: 10.3389/fmicb.2021.687463
https://doi.org/10.3389/fmicb.2021.687463
Wang L., Lin H., Dong Y., Li B., He Y. (2020): Effects of endophytes inoculation on rhizosphere and endosphere microecology of Indian mustard (Brassica juncea) grown in vanadium-contaminated soil and its enhancement on phytoremediation. Chemosphere, 240: 124891. doi: 10.1016/j.chemosphere.2019.124891
https://doi.org/10.1016/j.chemosphere.2019.124891
Weber T., Blin K., Duddela S., Krug D., Kim H.U., Bruccoleri R., Lee S.Y., Fischbach M.A., Müller R., Wohlleben W. (2015): antiSMASH 3.0 – A comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Research, 43: 237–243.
https://doi.org/10.1093/nar/gkv437
Westoby M., Nielsen D.A., Gillings M.R., Litchman E., Madin J.S., Paulsen I.T., Tetu S.G. (2021): Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea. Ecology and Evolution, 11: 3956–3976.
https://doi.org/10.1002/ece3.7290
Wu Y., Wang Y., Li J., Hu J., Chen K., Wei Y., Bazhanov D.P., Bazhanova A.A., Yang H. (2015): Draft genome sequence of Stenotrophomonas maltophilia strain B418, a promising agent for biocontrol of plant pathogens and root-knot nematode. Genome Announcements, 3: 15. doi: 10.1128/genomea.00015-15
https://doi.org/10.1128/genomeA.00015-15
Youseif S.H. (2018): Genetic diversity of plant growth promoting rhizobacteria and their effects on the growth of maize plants under greenhouse conditions. Annals of Agricultural Sciences, 63: 25–35.
https://doi.org/10.1016/j.aoas.2018.04.002
Zeng Q., Xie J., Li Y., Gao T., Xu C., Wang Q. (2018): Comparative genomic and functional analyses of four sequenced Bacillus cereus genomes reveal conservation of genes relevant to plant-growth-promoting traits. Scientific Reports, 8: 17009. doi: 10.1038/s41598-018-35300-y
https://doi.org/10.1038/s41598-018-35300-y
Zheng H., Mao Y., Teng J., Zhu Q., Ling J., Zhong Z. (2015): Flagellar-dependent motility in Mesorhizobium tianshanense is involved in the early stage of plant host interaction: Study of an flgE mutant. Current Microbiology, 70: 219–227.
https://doi.org/10.1007/s00284-014-0701-x
Zhu B., Liu H., Tian W.X., Fan X.Y., Li B., Zhou X.P., Jin G.L., Xie G.L. (2012): Genome sequence of Stenotrophomonas maltophilia RR-10, isolated as an endophyte from rice root. Journal of Bacteriology, 194: 1280–1281.
https://doi.org/10.1128/JB.06702-11