doi:10.48130/BPR-2023-0024

[1]

Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, et al. 2015. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiology & Molecular Biology Reviews Mmbr 79:293−320

doi: 10.1128/MMBR.00050-14

[2]

Miliute I, Buzaite O, Baniulis D, Stanys V. 2015. Bacterial endophytes in agricultural crops and their role in stress tolerance: A review. Zemdirbyste-Agriculture 102:465−78

doi: 10.13080/z-a.2015.102.060

[3]

Chen L, Shi H, Heng J, Wang D, Bian k. 2019. Antimicrobial, plant growth-promoting and genomic properties of the peanut endophyte Bacillus velezensis LDO2. Microbiological Research 218:41−48

doi: 10.1016/j.micres.2018.10.002

[4]

Wicaksono WA, Jones EE, Casonato S, Monk J, Ridgway HJ. 2018. Biological control of Pseudomonas syringae pv. actinidiae (Psa), the causal agent of bacterial canker of kiwifruit, using endophytic bacteria recovered from a medicinal plant. Biological Control 116:103−12

doi: 10.1016/j.biocontrol.2017.03.003

[5]

Woźniak M, Gałązka A, Tyśkiewicz R, Jaroszuk-Ściseł J. 2019. Endophytic bacteria potentially promote plant growth by synthesizing different metabolites and their phenotypic/physiological profiles in the biolog GEN III microPlate TM Test. International Journal of Molecular Sciences 20:5283

doi: 10.3390/ijms20215283

[6]

Taghavi S, van der Lelie D, Hoffman A, Zhang YB, Walla MD, et al. 2010. Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. Plos Genetics 6:e1000943

doi: 10.1371/journal.pgen.1000943

[7]

Bertalan M, Albano R, de Pádua V, Rouws L, Rojas C, et al. 2009. Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10:450

doi: 10.1186/1471-2164-10-450

[8]

Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, et al. 2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nature Biotechnology 25:1007−14

doi: 10.1038/nbt1325

[9]

Jia H, Xi Z, Ma J, Li Y, Hao C, et al. 2022. Endophytic bacteria from the leaves of two types of albino tea plants, indicating the plant growth promoting properties. Plant Growth Regulation 96:331−41

doi: 10.1007/s10725-021-00779-5

[10]

Wang Y, Shu X, Hou J, Lu W, Zhao W, et al. 2018. Selenium nanoparticle synthesized by Proteus mirabilis YC801: An efficacious pathway for selenite biotransformation and detoxification. International Journal of Molecular Sciences 19:3809

doi: 10.3390/ijms19123809

[11]

Huang Y, Li W, Mo X. 2016. Comparative study on the preparation methods of transmission electron microscope negative staining specimens for plant endophyte. Journal of Guangxi Normal University (Natural ence Edition) 34:127−30

doi: 10.16088/j.issn.1001-6600.2016.03.018

[12]

Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods 13(12):1050

doi: 10.1038/nmeth.4035

[13]

Thompson D, Cognat V, Goodfellow M, Koechler S, Heintz D, et al. 2020. Phylogenomic classification and biosynthetic potential of the fossil fuel-Biodesulfurizing Rhodococcus Strain IGTS8. Frontiers in Microbiology 11:1417

doi: 10.3389/fmicb.2020.01417

[14]

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, et al. 2021. Pfam: The protein families database in 2021. Nucleic Acids Research 49:D412−D419

doi: 10.1093/nar/gkaa913

[15]

Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, et al. 2017. AntiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Research 45:W36−W41

doi: 10.1093/nar/gkx319

[16]

Cheung J, Hendrickson WA. 2010. Sensor domains of two-component regulatory systems. Current Opinion in Microbiology 13:116−23

doi: 10.1016/j.mib.2010.01.016

[17]

Insuk C, Kuncharoen N, Cheeptham N, Tanasupawat S, Pathom-aree W. 2020. Bryophytes harbor cultivable actinobacteria with plant growth promoting potential. Frontiers in Microbiology 11:563047

doi: 10.3389/fmicb.2020.563047

[18]

Ludueña LM, Anzuay MS, Angelini JG, McIntosh M, Becker A, et al. 2019. Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Genomics 111:913−20

doi: 10.1016/j.ygeno.2018.05.021

[19]

Emms D, Kelly S. 2018. STAG: Species tree inference from all genes. Cold Spring Harbor Laboratory bioRxiv:Preprint

doi: 10.1101/267914

[20]

Cui Z, Huntley RB, Schultes NP, Steven B, Zeng Q. 2021. Inoculation of stigma-colonizing microbes to apple stigmas alters microbiome structure and reduces the occurrence of fire blight disease. Phytobiomes Journal 5:156−65

doi: 10.1094/pbiomes-04-20-0035-r

[21]

Wang J, Han W, Pan Y, Guo A, Zhang D, et al. 2022. First report of stalk rot of celery caused by Erwinia rhapontici in China. Plant Disease 106:1513

doi: 10.1094/PDIS-07-21-1364-PDN

[22]

Li L, Li H, Shi Y, Chai AL, Xie X, Li B. 2020. First report of bacterial leaf spot of cucurbita pepo caused by Erwinia persicina in China. Plant Disease 105:1558

doi: 10.1094/PDIS-06-20-1241-PDN

[23]

Kube M, Migdoll AM, Müller I, Kuhl H, Beck A, et al. 2008. The Genome of Erwinia tasmaniensis strain Et1/99, a non-pathogenic bacterium in the genus Erwinia. Environmental Microbiology 10:2211−22

doi: 10.1111/j.1462-2920.2008.01639.x

[24]

Rosconi F, Souza EM, Pedrosa FD, Platero RA, González C, et al. 2006. Iron depletion affects nitrogenase activity and expression of nifH and nifA genes in Herbaspirillum seropedicae. FEMS Microbiology Letters 258:214−19

doi: 10.1111/j.1574-6968.2006.00218.x

[25]

Buchfink B, Reuter K, Drost HG. 2021. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature Methods 18:366−68

doi: 10.1038/s41592-021-01101-x

[26]

Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome research 13:2178−89

doi: 10.1101/gr.1224503

[27]

Carroll CS, Moore MM. 2018. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Critical Reviews in Biochemistry & Molecular Biology 53:356−81

doi: 10.1080/10409238.2018.1476449

[28]

Rossi-Tamisier M, Benamar S, Raoult D, Fournier PE. 2015. Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. International Journal of Systematic and Evolutionary Microbiology 65:1929

doi: 10.1099/ijs.0.000161

[29]

Yang L, Zhi X, Li W. 2008. Phylogenetic analysis of nocardiopsis species based on 16S rRNA, gyrB, sod and rpoB gene sequences. Acta Microbiologica Sinica 47:951−55

doi: 10.3321/j.issn:0001-6209.2007.06.002

[30]

Zuo G, Qi J, Hao B. 2018. Polyphyly in 16S rRNA-based LVTree versus monophyly in whole-genome-based CVTree. Genomics, Proteomics & Bioinformatics 16:310−19

doi: 10.1016/j.gpb.2018.06.005

[31]

Gomila M, Busquets A, Mulet M, García-Valdés E, Lalucat J. 2017. Clarification of taxonomic status within the Pseudomonas syringae species group based on a phylogenomic analysis. Frontiers in microbiology 8:2422

doi: 10.3389/fmicb.2017.02422

[32]

Goordial J, Raymond-Bouchard I, Zolotarov Y, de Bethencourt L, Ronholm J, et al. 2016. Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiology Ecology 92:fiv154

doi: 10.1093/femsec/fiv154

[33]

Becker M, Patz S, Becker Y, Berger B, Drungowski M, et al. 2018. Comparative genomics reveal a flagellar system, a Type VI secretion system and plant growth-promoting gene clusters unique to the endophytic bacterium Kosakonia radicincitans. Frontiers in Microbiology 9:1997

doi: 10.3389/fmicb.2018.01997

[34]

Mano Y, Nemoto K. 2012. The pathway of auxin biosynthesis in plants. Journal of Experimental Botany 63:2853−72

doi: 10.1093/jxb/ers091

[35]

Lin WJ, Ho HC, Chu SC, Chou JY. 2020. Effects of auxin derivatives on phenotypic plasticity and stress tolerance in five species of the green alga Desmodesmus (Chlorophyceae, Chlorophyta). PeerJ 8:e8623

doi: 10.7717/peerj.8623

[36]

Wagh J, Shah S, Bhandari P, Archana G, Kumar GN. 2014. Heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to Herbaspirillum seropedicae Z67. Applied Microbiology and Biotechnology 98:5117−29

doi: 10.1007/s00253-014-5610-1

[37]

Jain A, Das S. 2016. Insight into the Interaction between Plants and Associated Fluorescent Pseudomonas spp. International Journal of Agronomy 2016:1−8

doi: 10.1155/2016/4269010

[38]

Carroll CS, Moore MM. 2018. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Critical Reviews in Biochemistry and Molecular Biology 53:356−81

doi: 10.1080/10409238.2018.1476449

[39]

Gu S, Wei Z, Shao Z, Friman VP, Cao K, et al. 2020. Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nature Microbiology 5:1002−10

doi: 10.1038/s41564-020-0719-8

[40]

Zinchenko V. 1999. Genetic regulation of nitrogen assimilation in photosynthetic bacteria. Genetika 35:1495-510. www.mendeley.com/catalogue/7ebeefad-f93e-34f6-b250-712d2b076b0a/

[41]

Todorovic B, Glick BR. 2008. The interconversion of ACC deaminase and D-cysteine desulfhydrase by directed mutagenesis. Planta 229:193−205

doi: 10.1007/s00425-008-0820-3

[42]

Zhang Z, Yao Q, Wang L. 2010. Expression of yeast Hem1 controlled by Arabidopsis HemA1 promoter enhances leaf photosynthesis in transgenic tobacco. Molecular Biology Reports 38:4369−79

doi: 10.1007/s11033-010-0564-6

[43]

Boels IC, Ramos A, Kleerebezem M, de Vos WM. 2001. Functional analysis of the Lactococcus lactis galU and galE genes and their impact on sugar nucleotide and exopolysaccharide biosynthesis. Applied and Environmental Microbiology 67:3033−40

doi: 10.1128/AEM.67.7.3033-3040.2001

[44]

Wang X, Liang H, Wang S, Fang W, Xu J, et al. 2019. Function of Copper-Resistant Gene copA of Ralstonia solanacearum. Scientia Agricultura Sinica 52:837−48

doi: 10.3864/j.issn.0578-1752.2019.05.006

[45]

Behera BK, Chakraborty HJ, Patra B, Rout AK, Dehury B, et al. 2020. Metagenomic analysis reveals bacterial and fungal diversity and their bioremediation potential from sediments of river Ganga and Yamuna in India. Frontiers in Microbiology 11:556136

doi: 10.3389/fmicb.2020.556136

[46]

Subramanian Vignesh K, Deepe GS Jr. 2017. Metallothioneins: emerging modulators in immunity and infection. International Journal of Molecular Sciences 18:2197

doi: 10.3390/ijms18102197

[47]

Allocati N, Federici L, Masulli M, Di Ilio C. 2009. Glutathione transferases in bacteria. The FEBS Journal 276:58−75

doi: 10.1111/j.1742-4658.2008.06743.x

[48]

Ali M, Ali Q, Sohail MA, Ashraf MF, Saleem MH, et al. 2021. Diversity and taxonomic distribution of endophytic bacterial community in the rice plant and its prospective. International Journal of Molecular Science 22:10165

doi: 10.3390/ijms221810165

[49]

Neumann S, Wynen A, Trüper H, Dahl C. 2000. Characterization of the cys gene locus from Allochromatium vinosum indicates an unusual sulfate assimilation pathway. Molecular Biology Reports 27:27−33

doi: 10.1023/A:1007058421714

[50]

Bacilio-Jiménez M, Aguilar-Flores S, Ventura-Zapata E, Pérez-Campos E, Bouquelet S, et al. 2003. Chemical characterization of root exudates from rice (Oryza sativa) and their effects on the chemotactic response of endophytic bacteria. Plant and Soil 249:271−77

doi: 10.1023/A:1022888900465

[51]

Merritt PM, Danhorn T, Fuqua C. 2007. Motility and chemotaxis in Agrobacterium tumefaciens surface attachment and biofilm formation. Journal of Bacteriology 189:8005−14

doi: 10.1128/JB.00566-07

[52]

Thormann KM, Saville RM, Shukla S, Pelletier DA, Spormann AM. 2004. Initial phases of biofilm formation in Shewanella oneidensis MR-1. Journal of Bacteriology 186:8096−104

doi: 10.1128/JB.186.23.8096-8104.2004

[53]

Bubendorfer S, Koltai M, Rossmann F, Sourjik V, Thormann KM. 2014. Secondary bacterial flagellar system improves bacterial spreading by increasing the directional persistence of swimming. PNAS 111:11485−90

doi: 10.1073/pnas.1405820111

[54]

Santos-Beneit F. 2015. The Pho regulon: A huge regulatory network in bacteria. Frontiers in Microbiology 6:402

doi: 10.3389/fmicb.2015.00402

[55]

Wang Y, Lou H, Wang H, Hu W, Yan J. 2011. CheA/CheY signaling system responsible for chemotaxis in vitro and colonization in vivo of Campylobacter jejuni. Chinese Journal of Microbiology and Immunology 31:201−7

doi: 10.3760/cma.j.issn.0254-5101.2011.03.003

[56]

Zúñiga A, Poupin MJ, Donoso R, Ledger T, Guiliani N, et al. 2013. Quorum Sensing and indole-3-acetic acid degradation play a role in colonization and plant growth promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN. Molecular Plant-microbe Interactions 26:546−53

doi: 10.1094/MPMI-10-12-0241-R