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AIMS Microbiology

2017, Volume 3, Issue 3: 383-412. doi: 10.3934/microbiol.2017.3.383
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Taxonomy and systematics of plant probiotic bacteria in the genomic era

  • School of Biology, Newcastle University, Newcastle upon Tyne, UK
  • Received: 03 March 2017 Accepted: 22 May 2017 Published: 31 May 2017

  • Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.

    Citation: Lorena Carro, Imen Nouioui. Taxonomy and systematics of plant probiotic bacteria in the genomic era[J]. AIMS Microbiology, 2017, 3(3): 383-412. doi: 10.3934/microbiol.2017.3.383

    Related Papers:

  • Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.


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    [1] Hill C, Guarner F, Reid G, et al. (2014) Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11: 506–514. doi: 10.1038/nrgastro.2014.66
    [2] Redman RS, Kim YO, Woodward CJ, et al. (2011) Increased fitness of rice plants to abiotic stress via habitat adapted symbiosis: a strategy for mitigating impacts of climate change. PLoS One 6: e14823. doi: 10.1371/journal.pone.0014823
    [3] Xie J, Shi H, Du Z, et al. (2016) Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species. Sci Rep 6: 21329. doi: 10.1038/srep21329
    [4] Felis GE, Dellaglio F, Torriani S (2009) Taxonomy of Probiotic Microorganisms, In: Charalampopoulos D, Rastall RA, Editors, Prebiotics and Probiotics Science and Technology, New York: Springer New York, 591–637.
    [5] Bull M, Plummer S, Marchesi J, et al. (2013) The life history of Lactobacillus acidophilus as a probiotic: a tale of revisionary taxonomy, misidentification and commercial success. FEMS Microbiol Lett 349: 77–87. doi: 10.1111/1574-6968.12293
    [6] Felis GE, Dellaglio F (2007) Taxonomy of Lactobacilli and Bifidobacteria. Curr Issues Intest Microbiol 8: 44–61.
    [7] Vandamme P, Pot B, Gillis M, et al. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60: 407–438.
    [8] Williams JG, Kubelik AR, Livak KJ, et al. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18: 6531–6535. doi: 10.1093/nar/18.22.6531
    [9] Versalovic J, Koeuth T, Lupski JR (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19: 6823–6831. doi: 10.1093/nar/19.24.6823
    [10] Versalovic J, Schneider M, De Bruijn FJ, et al. (1994) Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Method Mol Cell Biol 5: 25–40.
    [11] Laguerre G, Allard MR, Revoy F, et al. (1994) Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microb 60: 56–63.
    [12] Carro L, Sproer C, Alonso P, et al. (2012) Diversity of Micromonospora strains isolated from nitrogen fixing nodules and rhizosphere of Pisum sativum analyzed by multilocus sequence analysis. Syst Appl Microbiol 35: 73–80. doi: 10.1016/j.syapm.2011.11.003
    [13] Trujillo ME, Alonso-Vega P, Rodriguez R, et al. (2010) The genus Micromonospora is widespread in legume root nodules: the example of Lupinus angustifolius. ISME J 4: 1265–1281. doi: 10.1038/ismej.2010.55
    [14] Singh BP (2015) Molecular and functional diversity of PGPR fluorescent Pseudomonads based on 16S rDNA-RFLP and RAPD markers. J Environ Biol 36: 1169–1178.
    [15] Gaunt MW, Turner SL, Rigottier-Gois L, et al. (2001) Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Micr 51: 2037–2048. doi: 10.1099/00207713-51-6-2037
    [16] Perez-Yepez J, Armas-Capote N, Velazquez E, et al. (2014) Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: Resolving the taxonomic affiliation of the Cicer canariense rhizobia. Syst Appl Microbiol 37: 553–559. doi: 10.1016/j.syapm.2014.10.003
    [17] Ribeiro RA, Barcellos FG, Thompson FL, et al. (2009) Multilocus sequence analysis of Brazilian Rhizobium microsymbionts of common bean (Phaseolus vulgaris L.) reveals unexpected taxonomic diversity. Res Microbiol 160: 297–306.
    [18] Bennasar A, Mulet M, Lalucat J, et al. (2010) PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species. BMC Microbiol 10: 118. doi: 10.1186/1471-2180-10-118
    [19] Jang MA, Koh WJ, Huh HJ, et al. (2014) Distribution of nontuberculous mycobacteria by multigene sequence-based typing and clinical significance of isolated strains. J Clin Microbiol 52: 1207–1212. doi: 10.1128/JCM.03053-13
    [20] Kampfer P, Glaeser SP (2016) Serratia aquatilis sp. nov., isolated from drinking water systems. Int J Syst Evol Micr 66: 407–413.
    [21] Marrero G, Schneider KL, Jenkins DM, et al. (2013) Phylogeny and classification of Dickeya based on multilocus sequence analysis. Int J Syst Evol Micr 63: 3524–3539. doi: 10.1099/ijs.0.046490-0
    [22] Martens M, Dawyndt P, Coopman R, et al. (2008) Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Micr 58: 200–214. doi: 10.1099/ijs.0.65392-0
    [23] Naser SM, Thompson FL, Hoste B, et al. (2005) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151: 2141–2150. doi: 10.1099/mic.0.27840-0
    [24] Sen A, Daubin V, Abrouk D, et al. (2014) Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders "Frankiales" and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Micr 64: 3821–3832.
    [25] Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Bacteriol 44: 846–849.
    [26] Wayne LG, Brenner DJ, Colwell RR, et al. (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Micr 37: 463–464.
    [27] Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102: 2567–2572. doi: 10.1073/pnas.0409727102
    [28] Tindall BJ, Rossello-Mora R, Busse HJ, et al. (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Micr 60: 249–266. doi: 10.1099/ijs.0.016949-0
    [29] Stephens ZD, Lee SY, Faghri F, et al. (2015) Big data: Astronomical or genomical? PloS Biol 13: e1002195. doi: 10.1371/journal.pbio.1002195
    [30] Lopez-Modéjar R, Kostovčík M, Lladó S, et al. (2017) Exploring the Plant Microbiome Through Multi-omics Approaches, In: Kumar V, Kumar M, Sharma S, et al., Editors, Probiotics in Agroecosystem, Springer Nature.
    [31] Ipci K, Altıntoprak N, Muluk NB, et al. (2017) The possible mechanisms of the human microbiome in allergic diseases. Eur Arch Oto-Rhino-L 274: 617–626.
    [32] Kadakkuzha BM, Puthanveettil SV (2013) Genomics and proteomics in solving brain complexity. Mol Biosyst 9: 1807–1821. doi: 10.1039/c3mb25391k
    [33] Bruto M, Prigent-Combaret C, Muller D, et al. (2014) Analysis of genes contributing to plant-beneficial functions in plant growth-promoting rhizobacteria and related Proteobacteria. Sci Rep 4: 6261.
    [34] Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5: 216.
    [35] Kumar V, Baweja M, Singh PK, et al. (2016) Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions. Front Plant Sci 7.
    [36] RB P (1974) Probiotics, the other half of the antibiotic story. Anim Nutr Health 29: 4.
    [37] Fuller R (1989) Probiotics in man and animals. J Appl Bacteriol 66: 365–378. doi: 10.1111/j.1365-2672.1989.tb05105.x
    [38] Sessitsch A, Hardoim P, Doring J, et al. (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant Microbe In 25: 28–36. doi: 10.1094/MPMI-08-11-0204
    [39] Akinsanya MA, Goh JK, Lim SP, et al. (2015) Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genomics Data 6: 159–163. doi: 10.1016/j.gdata.2015.09.004
    [40] Muller CA, Obermeier MM, Berg G (2016) Bioprospecting plant-associated microbiomes. J Biotechnol 235: 171–180. doi: 10.1016/j.jbiotec.2016.03.033
    [41] Bertani I, Abbruscato P, Piffanelli P, et al. (2016) Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis. Environ Microbiol Rep 8: 388–398. doi: 10.1111/1758-2229.12403
    [42] Kolton M, Sela N, Elad Y, et al. (2013) Comparative genomic analysis indicates that niche adaptation of terrestrial Flavobacteria is strongly linked to plant glycan metabolism. PLoS One 8: e76704. doi: 10.1371/journal.pone.0076704
    [43] Hartman K, van der Heijden MG, Roussely-Provent V, et al. (2017) Deciphering composition and function of the root microbiome of a legume plant. Microbiome 5: 2.
    [44] Shade A, McManus PS, Handelsman J (2013) Unexpected diversity during community succession in the apple flower microbiome. mBio 4: e00602–e00612.
    [45] Garrity GM (2005) Volume 2: The Proteobacteria, In: Garrity GM, Editor, Bergey's Manual of Systematic Bacteriology, Springer.
    [46] van der Heijden MG, Hartmann M (2016) Networking in the plant microbiome. PLoS Biol 14: e1002378. doi: 10.1371/journal.pbio.1002378
    [47] Kaul S, Sharma T, Dhar MK (2016) "Omics" tools for better understanding the plant–endophyte interactions. Front Plant Sci 7.
    [48] Liu H, Carvalhais LC, Schenk PM, et al. (2017) Effects of jasmonic acid signalling on the wheat microbiome differ between body sites. Sci Rep 7: 41766.
    [49] Leite J, Fischer D, Rouws LFM, et al. (2017) Cowpea nodules harbor non-rhizobial bacterial communities that are shaped by soil type rather than plant genotype. Front Plant Sci 7.
    [50] Zgadzaj R, Garrido-Oter R, Jensen DB, et al. (2016) Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Natl Acad Sci USA 113: E7996–E8005.
    [51] Xiao X, Chen W, Zong L, et al. (2017) Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments. Mol Ecol 26: 1641–1651. doi: 10.1111/mec.14027
    [52] Foo JL, Ling H, Lee YS, et al. (2017) Microbiome engineering: Current applications and its future. Biotech J: 1600099-n/a.
    [53] Ushio M, Yamasaki E, Takasu H, et al. (2015) Microbial communities on flower surfaces act as signatures of pollinator visitation. Sci Rep 5: 8695. doi: 10.1038/srep08695
    [54] Paterson J, Jahanshah G, Li Y, et al. (2016) The contribution of genome mining strategies to the understanding of active principles of PGPR strains. FEMS Microbiol Ecol 93: fiw249–fiw249.
    [55] Reeve W, Ardley J, Tian R, et al. (2015) A genomic encyclopedia of the root nodule bacteria: assessing genetic diversity through a systematic biogeographic survey. Stand Genomic Sci 10: 14. doi: 10.1186/1944-3277-10-14
    [56] Seshadri R, Reeve WG, Ardley JK, et al. (2015) Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria. Sci Rep 5: 16825. doi: 10.1038/srep16825
    [57] Redondo-Nieto M, Barret M, Morrissey J, et al. (2013) Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genomics 14: 54. doi: 10.1186/1471-2164-14-54
    [58] Garrido-Sanz D, Meier-Kolthoff JP, Goker M, et al. (2016) Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 11: e0150183. doi: 10.1371/journal.pone.0150183
    [59] Simon S, Petrasek J (2011) Why plants need more than one type of auxin. Plant Sci 180: 454–460. doi: 10.1016/j.plantsci.2010.12.007
    [60] Gupta S, Ellis SE, Ashar FN, et al. (2014) Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nat Commun 5: 5748. doi: 10.1038/ncomms6748
    [61] Cecagno R, Fritsch TE, Schrank IS (2015) The plant growth-promoting bacteria Azospirillum amazonense: genomic versatility and phytohormone pathway. Biomed Res Int 2015: 898592.
    [62] Franco CM, Araujo R, Adetutu E, et al. (2016) Complete genome sequences of the endophytic Streptomyces strains EN16, EN23, and EN27, isolated from wheat plants. Genome Announc 4: e01342-16.
    [63] Hirsch AM, Alvarado J, Bruce D, et al. (2013) Complete genome sequence of Micromonospora strain L5, a potential plant-growth-regulating Actinomycete, originally isolated from Casuarina equisetifolia root nodules. Genome Announc 1: e00759-13.
    [64] Klingeman DM, Utturkar S, Lu TY, et al. (2015) Draft genome sequences of four Streptomyces isolates from the Populus trichocarpa root endosphere and rhizosphere. Genome Announc 3: e01344-15.
    [65] Bravo JI, Lozano GL, Handelsman J (2017) Draft genome sequence of Flavobacterium johnsoniae CI04, an isolate from the soybean rhizosphere. Genome Announc 5: e01535-16.
    [66] Trujillo ME, Bacigalupe R, Pujic P, et al. (2014) Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style? PLoS One 9: e108522. doi: 10.1371/journal.pone.0108522
    [67] Zhang N, Yang D, Kendall JR, et al. (2016) Comparative genomic analysis of Bacillus amyloliquefaciens and Bacillus subtilis reveals evolutional traits for adaptation to plant-associated habitats. Front Microbiol 7: 2039.
    [68] Kim SY, Lee SY, Weon HY, et al. (2017) Complete genome sequence of Bacillus velezensis M75, a biocontrol agent against fungal plant pathogens, isolated from cotton waste. J Biotechnol 241: 112–115. doi: 10.1016/j.jbiotec.2016.11.023
    [69] Cai XC, Liu CH, Wang BT, et al. (2017) Genomic and metabolic traits endow Bacillus velezensis CC09 with a potential biocontrol agent in control of wheat powdery mildew disease. Microbiol Res 196: 89–94. doi: 10.1016/j.micres.2016.12.007
    [70] Whitman WB, Woyke T, Klenk HP, et al. (2015) Genomic encyclopedia of bacterial and archaeal type strains, phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci 10: 26. doi: 10.1186/s40793-015-0017-x
    [71] Holzapfel WH, Haberer P, Geisen R, et al. (2001) Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr 73: 365S–373S.
    [72] Chan JZ, Halachev MR, Loman NJ, et al. (2012) Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12: 302. doi: 10.1186/1471-2180-12-302
    [73] Daubin V, Gouy M, Perriere G (2002) A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12: 1080–1090. doi: 10.1101/gr.187002
    [74] Comas I, Moya A, González-Candelas F (2007) From phylogenetics to phylogenomics: The evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Syst Biol 56: 1–16.
    [75] Herniou EA, Luque T, Chen X, et al. (2001) Use of whole genome sequence data to infer baculovirus phylogeny. J Virol 75: 8117–8126. doi: 10.1128/JVI.75.17.8117-8126.2001
    [76] Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21: 108–110. doi: 10.1038/5052
    [77] Gu X, Zhang H (2004) Genome phylogenetic analysis based on extended gene contents. Mol Biol Evol 21: 1401–1408. doi: 10.1093/molbev/msh138
    [78] Karlin S, Mrazek J, Campbell AM (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179: 3899–3913. doi: 10.1128/jb.179.12.3899-3913.1997
    [79] Pride DT, Meinersmann RJ, Wassenaar TM, et al. (2003) Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 13: 145–158. doi: 10.1101/gr.335003
    [80] House CH, Fitz-Gibbon ST (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54: 539–547. doi: 10.1007/s00239-001-0054-5
    [81] Fitz-Gibbon ST, House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27: 4218–4222. doi: 10.1093/nar/27.21.4218
    [82] Wolf YI, Rogozin IB, Kondrashov AS, et al. (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res 11: 356–372. doi: 10.1101/gr.GR-1619R
    [83] Coenye T, Gevers D, Van de Peer Y, et al. (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29: 147–167. doi: 10.1016/j.fmrre.2004.11.004
    [84] Wisniewski-Dye F, Borziak K, Khalsa-Moyers G, et al. (2011) Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet 7: e1002430.
    [85] Jordan EOA (1890) A report on certain species of bacteria observed in sewage.
    [86] Hoffmann H, Stindl S, Ludwig W, et al. (2005) Reassignment of enterobacter dissolvens to Enterobacter cloacae as E. cloacae subspecies dissolvens comb. nov. and emended description of Enterobacter asburiae and Enterobacter kobei. Syst Appl Microbiol 28: 196–205.
    [87] V T (1895) I. Generi e le Specie delle Batteriacee, Zanaboni and Gabuzzi, Milano, 1889. 2 MIGULA (W.): Schizomycetes (Bacteria, Bacterien). Teil I, Abteilung Ia, Teil I, Abteilung Ia,.
    [88] Blomqvist K, Nikkola M, Lehtovaara P, et al. (1993) Characterization of the genes of the 2,3-butanediol operons from Klebsiella terrigena and Enterobacter aerogenes. J Bacteriol 175: 1392–1404. doi: 10.1128/jb.175.5.1392-1404.1993
    [89] Renna MC, Najimudin N, Winik LR, et al. (1993) Regulation of the Bacillus subtilis alsS, alsD, and alsR genes involved in post-exponential-phase production of acetoin. J Bacteriol 175: 3863–3875. doi: 10.1128/jb.175.12.3863-3875.1993
    [90] Vinatzer BA, Weisberg AJ, Monteil CL, et al. (2017) A proposal for a genome similarity-based taxonomy for plant-pathogenic bacteria that is sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to Pseudomonas syringae sensu lato as a proof of concept. Phytopathology 107: 18–28. doi: 10.1094/PHYTO-07-16-0252-R
    [91] Euzeby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the internet. Int J Syst Bacteriol 47: 590–592. doi: 10.1099/00207713-47-2-590
    [92] Bruto M, Prigent-Combaret C, Muller D, et al. (2014) Analysis of genes contributing to plant-beneficial functions in Plant Growth-Promoting Rhizobacteria and related Proteobacteria. Sci Rep 4: 6261.
    [93] Poupin MJ, Timmermann T, Vega A, et al. (2013) Effects of the plant growth-promoting bacterium Burkholderia phytofirmans PsJN throughout the life cycle of Arabidopsis thaliana. PLoS One 8: e69435. doi: 10.1371/journal.pone.0069435
    [94] Sawana A, Adeolu M, Gupta RS (2014) Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 5: 429.
    [95] Cheng Q (2008) Perspectives in biological nitrogen fixation research. J Integr Plant Biol 50: 786–798. doi: 10.1111/j.1744-7909.2008.00700.x
    [96] Ormeño-Orrillo E, Servin-Garciduenas LE, Rogel MA, et al. (2015) Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics. Syst Appl Microbiol 38: 287–291.
    [97] Mousavi SA, Willems A, Nesme X, et al. (2015) Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 38: 84–90.
    [98] Benson DR, Silvester WB (1993) Biology of Frankia strains, actinomycete symbionts of actinorhizal plants. Microbiol Rev 57: 293–319.
    [99] Armas-Capote N, Perez-Yepez J, Martinez-Hidalgo P, et al. (2014) Core and symbiotic genes reveal nine Mesorhizobium genospecies and three symbiotic lineages among the rhizobia nodulating Cicer canariense in its natural habitat (La Palma, Canary Islands). Syst Appl Microbiol 37: 140–148.
    [100] Udwary DW, Gontang EA, Jones AC, et al. (2011) Significant natural product biosynthetic potential of actinorhizal symbionts of the genus Frankia, as revealed by comparative genomic and proteomic analyses. Appl Environ Microbiol 77: 3617–3625. doi: 10.1128/AEM.00038-11
    [101] Tisa LS, Beauchemin N, Gtari M, et al. (2013) What stories can the Frankia genomes start to tell us? J Biosci 38: 719–726. doi: 10.1007/s12038-013-9364-1
    [102] Clawson ML, Bourret A, Benson DR (2004) Assessing the phylogeny of Frankia-actinorhizal plant nitrogen-fixing root nodule symbioses with Frankia 16S rRNA and glutamine synthetase gene sequences. Mol Phylogenet Evol 31: 131–138. doi: 10.1016/j.ympev.2003.08.001
    [103] Jeong SC, Ritchie NJ, Myrold DD (1999) Molecular phylogenies of plants and Frankia support multiple origins of actinorhizal symbioses. Mol Phylogenet Evol 13: 493–503. doi: 10.1006/mpev.1999.0692
    [104] Gtari M, Daffonchio D, Boudabous A (2007) Assessment of the genetic diversity of Frankia microsymbionts of Elaeagnus angustifolia L. plants growing in a Tunisian date-palm oasis by analysis of PCR amplified nifD-K intergenic spacer. Can J Microbiol 53: 440–445.
    [105] Normand P, Orso S, Cournoyer B, et al. (1996) Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol 46: 1–9. doi: 10.1099/00207713-46-1-1
    [106] Cournoyer B, Lavire C (1999) Analysis of Frankia evolutionary radiation using glnII sequences. FEMS Microbiol Lett 177: 29–34. doi: 10.1111/j.1574-6968.1999.tb13709.x
    [107] Nouioui I, Ghodhbane-Gtari F, Beauchemin NJ, et al. (2011) Phylogeny of members of the Frankia genus based on gyrB, nifH and glnII sequences. Antonie Van Leeuwenhoek 100: 579–587.
    [108] Ghodhbane-Gtari F, Nouioui I, Chair M, et al. (2010) 16S-23S rRNA intergenic spacer region variability in the genus Frankia. Microb Ecol 60: 487–495. doi: 10.1007/s00248-010-9641-6
    [109] Normand P, Lapierre P, Tisa LS, et al. (2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17: 7–15.
    [110] Nouioui I, Del Carmen Montero-Calasanz M, Ghodhbane-Gtari F, et al. (2017) Frankia discariae sp. nov.: an infective and effective microsymbiont isolated from the root nodule of Discaria trinervis. Arch Microbiol: 1–7.
    [111] Nouioui I, Ghodhbane-Gtari F, Del Carmen Montero-Calasanz M, et al. (2017) Frankia inefficax sp. nov., an actinobacterial endophyte inducing ineffective, non nitrogen-fixing, root nodules on its actinorhizal host plants. Antonie Van Leeuwenhoek 110: 313–320.
    [112] Nouioui I, Ghodhbane-Gtari F, Rohde M, et al. (2017) Frankia coriariae sp. nov., an infective and effective microsymbiont isolated from Coriaria japonica. Int J Syst Evol Micr.
    [113] Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz MD, et al. (2016) Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Int J Syst Evol Micr 66: 5201–5210.
    [114] Woronin MS (1866) Über die bei der Schwarzerle (Alnus glutinosa) und bei der gewöhnlichen Garten-Lupine (Lupinus mutabilis) auftretenden Wurzelanschwellungen. Mem Acad Imp Sci St Petersbourg VII Series 10: 1–13.
    [115] Tubeuf K (1895) In Pflanzenkrankheiten durch Kryptogame Parasiten verursacht, Berlin: Verlag J Springer, 1–599.
    [116] Tisa LS, Oshone R, Sarkar I, et al. (2016) Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis 70: 5–16. doi: 10.1007/s13199-016-0390-2
    [117] Manzanera M, Santa-Cruz-Calvo L, Vilchez JI, et al. (2014) Genome sequence of Arthrobacter siccitolerans 4J27, a Xeroprotectant-producing desiccation-tolerant microorganism. Genome Announc 2: e00526-14.
    [118] Santacruz-Calvo L, Gonzalez-Lopez J, Manzanera M (2013) Arthrobacter siccitolerans sp. nov., a highly desiccation-tolerant, xeroprotectant-producing strain isolated from dry soil. Int J Syst Evol Micr 63: 4174–4180.
    [119] Koch C, Schumann P, Stackebrandt E (1995) Reclassification of Micrococcus agilis (Ali-Cohen 1889) to the genus Arthrobacter as Arthrobacter agilis comb. nov. and emendation of the genus Arthrobacter. Int J Syst Bacteriol 45: 837–839. doi: 10.1099/00207713-45-4-837
    [120] Singh RN, Gaba S, Yadav AN, et al. (2016) First high quality draft genome sequence of a plant growth promoting and cold active enzyme producing psychrotrophic Arthrobacter agilis strain L77. Stand Genomic Sci 11: 54. doi: 10.1186/s40793-016-0176-4
    [121] Lee JS, Lee KC, Pyun YR, et al. (2003) Arthrobacter koreensis sp. nov., a novel alkalitolerant bacterium from soil. Int J Syst Evol Micr 53: 1277–1280.
    [122] Manzanera M, Garcia-Fontana C, Vilchez JI, et al. (2015) Genome sequence of Rhodococcus sp. 4J2A2, a desiccation-tolerant bacterium involved in biodegradation of aromatic hydrocarbons. Genome Announc 3: e00592-15.
    [123] Narvaez-Reinaldo JJ, Barba I, Gonzalez-Lopez J, et al. (2010) Rapid method for isolation of desiccation-tolerant strains and xeroprotectants. Appl Environ Microbiol 76: 5254–5262.
    [124] Manzanera M, Narvaez-Reinaldo JJ, Garcia-Fontana C, et al. (2015) Genome sequence of Arthrobacter koreensis 5J12A, a plant growth-promoting and desiccation-tolerant strain. Genome Announc 3: e00648-15.
    [125] Hossain MJ, Ran C, Liu K, et al. (2015) Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum. Front Plant Sci 6: 631.
    [126] Hao K, He P, Blom J, et al. (2012) The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. J Bacteriol 194: 3264–3265.
    [127] Kim BK, Chung JH, Kim SY, et al. (2012) Genome sequence of the leaf-colonizing Bacterium Bacillus sp. strain 5B6, isolated from a cherry tree. J Bacteriol 194: 3758–3759.
    [128] Kloepper JW, Ryu CM, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94: 1259–1266. doi: 10.1094/PHYTO.2004.94.11.1259
    [129] Sumpavapol P, Tongyonk L, Tanasupawat S, et al. (2010) Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand. Int J Syst Evol Micr 60: 2364–2370.
    [130] Borriss R, Chen XH, Rueckert C, et al. (2011) Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int J Syst Evol Micr 61: 1786–1801.
    [131] Declercq AM, Haesebrouck F, Van den Broeck W, et al. (2013) Columnaris disease in fish: a review with emphasis on bacterium-host interactions. Vet Res 44: 27.
    [132] CE S (2011) Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum. J Adv Res 2: 97–108. doi: 10.1016/j.jare.2010.04.001
    [133] Sang MK CS, Kim KD (2008) Biological control of Phytophthora blight of pepper by antagonistic rhizobacteria selected from a sequential screening procedure. Biol Control 46: 424–433. doi: 10.1016/j.biocontrol.2008.03.017
    [134] Sang MK, Kim KD (2012) The volatile-producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. J Appl Microbiol 113: 383–398. doi: 10.1111/j.1365-2672.2012.05330.x
    [135] Fu Y, Tang X, Lai Q, et al. (2011) Flavobacterium beibuense sp. nov., isolated from marine sediment. Int J Syst Evol Micr 61: 205–209.
    [136] Jit S, Dadhwal M, Prakash O, et al. (2008) Flavobacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Micr 58: 1665–1669.
    [137] Bodenhausen N, Horton MW, Bergelson J (2013) Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 8: e56329. doi: 10.1371/journal.pone.0056329
    [138] Bulgarelli D, Rott M, Schlaeppi K, et al. (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488: 91–95. doi: 10.1038/nature11336
    [139] Lundberg DS, Lebeis SL, Paredes SH, et al. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488: 86–90. doi: 10.1038/nature11237
    [140] Kishi LT, Fernandes CC, Omori WP, et al. (2016) Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools. BMC Microbiol 16: 260.
    [141] Kim M, Lee KH, Yoon SW, et al. (2013) Analytical tools and databases for metagenomics in the next-generation sequencing era. Genomics Inform 11: 102–113. doi: 10.5808/GI.2013.11.3.102
    [142] Thompson CC, Amaral GR, Campeão M, et al. (2015) Microbial taxonomy in the post-genomic era: Rebuilding from scratch? Arch Microbiol 197: 359–370. doi: 10.1007/s00203-014-1071-2
    [143] Choi SC (2016) On the study of microbial transcriptomes using second- and third-generation sequencing technologies. J Microbiol 54: 527–536. doi: 10.1007/s12275-016-6233-2
    [144] Lu H, Giordano F, Ning Z (2016) Oxford nanopore minion sequencing and genome assembly. Genomics Proteomics Bioinformatics 14: 265–279. doi: 10.1016/j.gpb.2016.05.004
    [145] Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, et al. (2016) Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 7: 2003.
    [146] Bal HB, Das S, Dangar TK, et al. (2013) ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants. J Basic Microbiol 53: 972–984. doi: 10.1002/jobm.201200445
    [147] Upadhyay SK, Singh JS, Saxena AK, et al. (2012) Impact of PGPR inoculation on growth and antioxidant status of wheat under saline conditions. Plant Biology 14: 605–611. doi: 10.1111/j.1438-8677.2011.00533.x
    [148] Kim WI, Cho WK, Kim SN, et al. (2011) Genetic diversity of cultivable plant growth-promoting rhizobacteria in Korea. J Microbiol Biotechnol 21: 777–790. doi: 10.4014/jmb.1101.01031
    [149] Cardinale M, Ratering S, Suarez C, et al. (2015) Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress. Microbiol Res 181: 22–32.
    [150] Fabri S, Caucas V, Abril A (1996) Infectivity and effectiveness of different strains of Frankia spp. on Atriplex cordobensis plants. Rev Argent Microbiol 28: 31–38.
    [151] Salomon MV, Purpora R, Bottini R, et al. (2016) Rhizosphere associated bacteria trigger accumulation of terpenes in leaves of Vitis vinifera L. cv. Malbec that protect cells against reactive oxygen species. Plant Physiol Biochem 106: 295–304.
    [152] Banik A, Mukhopadhaya SK, Dangar TK (2016) Characterization of N2-fixing plant growth promoting endophytic and epiphytic bacterial community of Indian cultivated and wild rice (Oryza spp.) genotypes. Planta 243: 799–812.
    [153] Schwachtje J, Karojet S, Kunz S, et al. (2012) Plant-growth promoting effect of newly isolated rhizobacteria varies between two Arabidopsis ecotypes. Plant Signal Behav 7: 623–627. doi: 10.4161/psb.20176
    [154] Trujillo ME, Riesco R, Benito P, et al. (2015) Endophytic Actinobacteria and the interaction of Micromonospora and nitrogen fixing plants. Front Microbiol 6: 1341.
    [155] Solans M (2007) Discaria trinervis-Frankia symbiosis promotion by saprophytic actinomycetes. J Basic Microbiol 47: 243–250. doi: 10.1002/jobm.200610244
    [156] Goudjal Y, Toumatia O, Yekkour A, et al. (2014) Biocontrol of Rhizoctonia solani damping-off and promotion of tomato plant growth by endophytic actinomycetes isolated from native plants of Algerian Sahara. Microbiol Res 169: 59–65. doi: 10.1016/j.micres.2013.06.014
    [157] Anwar S, Ali B, Sajid I (2016) Screening of rhizospheric Actinomycetes for various in-vitro and in-vivo Plant Growth Promoting (PGP) traits and for agroactive compounds. Front Microbiol 7.
    [158] Gontia-Mishra I, Sapre S, Sharma A, et al. (2016) Amelioration of drought tolerance in wheat by the interaction of plant growth-promoting rhizobacteria. Plant Biol (Stuttg) 18: 992–1000. doi: 10.1111/plb.12505
    [159] Kolton M, Frenkel O, Elad Y, et al. (2014) Potential role of Flavobacterial gliding-motility and type IX secretion system complex in root colonization and plant defense. Mol Plant Microbe In 27: 1005–1013. doi: 10.1094/MPMI-03-14-0067-R
    [160] Tsavkelova EA, Cherdyntseva TA, Botina SG, et al. (2007) Bacteria associated with orchid roots and microbial production of auxin. Microbiol Res 162: 69–76. doi: 10.1016/j.micres.2006.07.014
    [161] Subramanian P, Kim K, Krishnamoorthy R, et al. (2016) Cold stress tolerance in psychrotolerant soil bacteria and their conferred chilling resistance in tomato (Solanum lycopersicum Mill.) under low temperatures. PLoS One 11: e0161592.
    [162] Simonetti E, Viso NP, Montecchia M, et al. (2015) Evaluation of native bacteria and manganese phosphite for alternative control of charcoal root rot of soybean. Microbiol Res 180: 40–48. doi: 10.1016/j.micres.2015.07.004
    [163] Kong HG, Kim BK, Song GC, et al. (2016) Aboveground whitefly infestation-mediated reshaping of the root microbiota. Front Microbiol 7.
    [164] Maynaud G, Willems A, Soussou S, et al. (2012) Molecular and phenotypic characterization of strains nodulating Anthyllis vulneraria in mine tailings, and proposal of Aminobacter anthyllidis sp. nov., the first definition of Aminobacter as legume-nodulating bacteria. Syst Appl Microbiol 35: 65–72.
    [165] Fasciglione G, Casanovas EM, Yommi A, et al. (2012) Azospirillum improves lettuce growth and transplant under saline conditions. J Sci Food Agri 92: 2518–2523. doi: 10.1002/jsfa.5661
    [166] Couillerot O, Ramírez-Trujillo A, Walker V, et al. (2013) Comparison of prominent Azospirillum strains in Azospirillum-Pseudomonas-Glomus consortia for promotion of maize growth. Appl Microbiol Biotech 97: 4639–4649. doi: 10.1007/s00253-012-4249-z
    [167] Chamam A, Sanguin H, Bellvert F, et al. (2013) Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association. Phytochemistry 87: 65–77. doi: 10.1016/j.phytochem.2012.11.009
    [168] Quiñones MA, Ruiz-Díez B, Fajardo S, et al. (2013) Lupinus albus plants acquire mercury tolerance when inoculated with an Hg-resistant Bradyrhizobium strain. Plant Physiol Biochem 73: 168–175. doi: 10.1016/j.plaphy.2013.09.015
    [169] Rivas R, Velázquez E, Willems A, et al. (2002) A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) Druce. Appl Environ Microbiol 68: 5217–5222.
    [170] Prabha C, Maheshwari DK, Bajpai VK (2013) Diverse role of fast growing rhizobia in growth promotion and enhancement of psoralen content in Psoralea corylifolia L. Pharmacognosy Mag 9: S57–S65.
    [171] Sorty AM, Meena KK, Choudhary K, et al. (2016) Effect of plant growth promoting bacteria associated with halophytic weed (Psoralea corylifolia L) on germination and seedling growth of wheat under saline conditions. Appl Biochem Biotech 180: 872–882. doi: 10.1007/s12010-016-2139-z
    [172] Brígido C, Glick BR, Oliveira S (2016) Survey of plant growth-promoting mechanisms in native Portuguese chickpea Mesorhizobium isolates. Microbial Ecol: 1–16.
    [173] Rangel WM, Thijs S, Janssen J, et al. (2017) Native rhizobia from Zn mining soil promote the growth of Leucaena leucocephala on contaminated soil. Int J Phytoremediation 19: 142–156. doi: 10.1080/15226514.2016.1207600
    [174] Kechid M, Desbrosses G, Rokhsi W, et al. (2013) The NRT2.5 and NRT2.6 genes are involved in growth promotion of Arabidopsis by the plant growth-promoting rhizobacterium (PGPR) strain Phyllobacterium brassicacearum STM196. New Phytol 198: 514–524.
    [175] Santoro MV, Bogino PC, Nocelli N, et al. (2016) Analysis of plant growth-promoting effects of fluorescent Pseudomonas strains isolated from Mentha piperita rhizosphere and effects of their volatile organic compounds on essential oil composition. Front Microbiol 7: 1085.
    [176] Pandey S, Ghosh PK, Ghosh S, et al. (2013) Role of heavy metal resistant Ochrobactrum sp. and Bacillus spp. strains in bioremediation of a rice cultivar and their PGPR like activities. J Microbiol 51: 11–17.
    [177] Paulucci NS, Gallarato LA, Reguera YB, et al. (2015) Arachis hypogaea PGPR isolated from Argentine soil modifies its lipids components in response to temperature and salinity. Microbiol Res 173: 1–9. doi: 10.1016/j.micres.2014.12.012
    [178] Garcia-Fraile P, Carro L, Robledo M, et al. (2012) Rhizobium promotes non-legumes growth and quality in several production steps: towards a biofertilization of edible raw vegetables healthy for humans. PLoS One 7: e38122. doi: 10.1371/journal.pone.0038122
    [179] Amaresan N, Kumar K, Sureshbabu K, et al. (2014) Plant growth-promoting potential of bacteria isolated from active volcano sites of Barren Island, India. Lett Appl Microbiol 58: 130–137. doi: 10.1111/lam.12165
    [180] Borsodi AK, Barany A, Krett G, et al. (2015) Diversity and ecological tolerance of bacteria isolated from the rhizosphere of halophyton plants living nearby Kiskunsag soda ponds, Hungary. Acta Microbiol Immunol Hung 62: 183–197. doi: 10.1556/030.62.2015.2.8
    [181] Busse HJ (2016) Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int J Syst Evol Micr 66: 9–37.
    [182] Behrendt U, Ulrich A, Schumann P, et al. (2002) Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov. Int J Syst Evol Micr 52: 1441–1454.
    [183] Agarkova IV, Lambrecht PA, Vidaver AK, et al. (2012) Genetic diversity among Curtobacterium flaccumfaciens pv. flaccumfaciens populations in the American high plains. Can J Microbiol 58: 788–801.
    [184] Chimwamurombe PM, Gronemeyer JL, Reinhold-Hurek B (2016) Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings. FEMS Microbiol Ecol 92: fiw083. doi: 10.1093/femsec/fiw083
    [185] Tisa LS, Oshone R, Sarkar I, et al. (2016) Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis 70: 5–16. doi: 10.1007/s13199-016-0390-2
    [186] Fidalgo C, Riesco R, Henriques I, et al. (2016) Microbacterium diaminobutyricum sp. nov., isolated from Halimione portulacoides, which contains diaminobutyric acid in its cell wall, and emended description of the genus Microbacterium. Int J Syst Evol Micr 66: 4492–4500.
    [187] Landa BB, Mavrodi DM, Thomashow LS, et al. (2003) Interactions between strains of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens in the rhizosphere of wheat. Phytopathology 93: 982–994. doi: 10.1094/PHYTO.2003.93.8.982
    [188] Rong X, Huang Y (2012) Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 35: 7–18. doi: 10.1016/j.syapm.2011.10.004
    [189] Conn VM, Franco CM (2004) Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol 70: 1787–1794.
    [190] Zeng Z, Chen C, Du H, et al. (2015) High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes. Stand Genomic Scis 10: 92. doi: 10.1186/s40793-015-0084-z
    [191] Ashrafi R, Pulkkinen K, Sundberg LR, et al. (2015) A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates. BMC Microbiology 15: 243. doi: 10.1186/s12866-015-0576-4
    [192] Chen T, Chen Z, Ma GH, et al. (2014) Diversity and potential application of endophytic bacteria in ginger. Genet Mol Res 13: 4918–4931. doi: 10.4238/2014.July.4.6
    [193] Tian F, Ding Y, Zhu H, et al. (2009) Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere. Braz J Microbiol 40: 276–284. doi: 10.1590/S1517-83822009000200013
    [194] Mohkam M, Nezafat N, Berenjian A, et al. (2016) Identification of Bacillus probiotics isolated from soil rhizosphere using 16S rRNA, recA, rpoB gene sequencing and RAPD-PCR. Probiotics Antimicrob Proteins 8: 8–18. doi: 10.1007/s12602-016-9208-z
    [195] Fterich A, Mahdhi M, Caviedes MA, et al. (2011) Characterization of root-nodulating bacteria associated to Prosopis farcta growing in the arid regions of Tunisia. Arch Microbiol 193: 385–397. doi: 10.1007/s00203-011-0683-z
    [196] Yang JH, Liu HX, Zhu GM, et al. (2008) Diversity analysis of antagonists from rice-associated bacteria and their application in biocontrol of rice diseases. J Appl Microbiol 104: 91–104.
    [197] Phi QT, Park YM, Seul KJ, et al. (2010) Assessment of root-associated Paenibacillus polymyxa groups on growth promotion and induced systemic resistance in pepper. J Microbiol Biotechnol 20: 1605–1613.
    [198] Ettoumi B, Guesmi A, Brusetti L, et al. (2013) Microdiversity of deep-sea Bacillales isolated from Tyrrhenian sea sediments as revealed by ARISA, 16S rRNA gene sequencing and BOX-PCR fingerprinting. Microbes Environ 28: 361–369. doi: 10.1264/jsme2.ME13013
    [199] Albert RA, Archambault J, Lempa M, et al. (2007) Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov. Int J Syst Evol Microbiol 57: 2729–2737.
    [200] Li L, Wieme A, Spitaels F, et al. (2014) Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis. Int J Syst Evol Micr 64: 2407–2415.
    [201] Gomila M, Prince-Manzano C, Svensson-Stadler L, et al. (2014) Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses. PLoS One 9: e114356.
    [202] Velazquez E, Rojas M, Lorite MJ, et al. (2008) Genetic diversity of endophytic bacteria which could be find in the apoplastic sap of the medullary parenchym of the stem of healthy sugarcane plants. J Basic Microbiol 48: 118–124. doi: 10.1002/jobm.200700161
    [203] Roger F, Marchandin H, Jumas-Bilak E, et al. (2012) Multilocus genetics to reconstruct aeromonad evolution. BMC Microbiol 12: 62. doi: 10.1186/1471-2180-12-62
    [204] Procopio RE, Araujo WL, Maccheroni Jr W, et al. (2009) Characterization of an endophytic bacterial community associated with Eucalyptus spp. Genet Mol Res 8: 1408–1422. doi: 10.4238/vol8-4gmr691
    [205] Reinhardt EL, Ramos PL, Manfio GP, et al. (2008) Molecular characterization of nitrogen-fixing bacteria isolated from brazilian agricultural plants at Sao Paulo state. Braz J Microbiol 39: 414–422. doi: 10.1590/S1517-83822008000300002
    [206] Capoen W, Den Herder J, Rombauts S, et al. (2007) Comparative transcriptome analysis reveals common and specific tags for root hair and crack-entry invasion in Sesbania rostrata. Plant Physiol 144: 1878–1889. doi: 10.1104/pp.107.102178
    [207] Lenart-Boron AM, Wolny-Koladka KA, Boron PM, et al. (2014) The molecular marker-based comparison of Azotobacter spp. populations isolated from industrial soils of Cracow-Nowa Huta steelworks (southern Poland) and the adjacent agricultural soils. J Environ Sci Health A Tox Hazard Subst Environ Eng 49: 1054–1063.
    [208] Rivas R, Martens M, de Lajudie P, et al. (2009) Multilocus sequence analysis of the genus Bradyrhizobium. Syst Appl Microbiol 32: 101–110. doi: 10.1016/j.syapm.2008.12.005
    [209] Ahnia H, Boulila F, Boulila A, et al. (2014) Cytisus villosus from Northeastern Algeria is nodulated by genetically diverse Bradyrhizobium strains. Antonie Van Leeuwenhoek 105: 1121–1129. doi: 10.1007/s10482-014-0173-9
    [210] Ong KS, Aw YK, Lee LH, et al. (2016) Burkholderia paludis sp. nov., an antibiotic-siderophore producing novel Burkholderia cepacia complex species, isolated from Malaysian tropical peat swamp soil. Front Microbiol 7: 2046.
    [211] Peeters C, Meier-Kolthoff JP, Verheyde B, et al. (2016) Phylogenomic study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 7: 877.
    [212] Rivas R, Willems A, Subba-Rao NS, et al. (2003) Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst Appl Microbiol 26: 47–53.
    [213] Duan YQ, Zhou XK, Di-Yan L, et al. (2015) Enterobacter tabaci sp. nov., a novel member of the genus Enterobacter isolated from a tobacco stem. Antonie Van Leeuwenhoek 108: 1161–1169.
    [214] Facey PD, Meric G, Hitchings MD, et al. (2015) Draft genomes, phylogenetic reconstruction, and comparative genomics of two novel cohabiting bacterial symbionts isolated from Frankliniella occidentalis. Genome Biol Evol 7: 2188–2202. doi: 10.1093/gbe/evv136
    [215] Izumi H, Anderson IC, Alexander IJ, et al. (2006) Endobacteria in some ectomycorrhiza of Scots pine (Pinus sylvestris). FEMS Microbiol Ecol 56: 34–43. doi: 10.1111/j.1574-6941.2005.00048.x
    [216] Kampfer P, McInroy JA, Doijad S, et al. (2016) Kosakonia pseudosacchari sp. nov., an endophyte of Zea mays. Syst Appl Microbiol 39: 1–7. doi: 10.1016/j.syapm.2015.09.004
    [217] Lu YL, Chen WF, Wang ET, et al. (2009) Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana species. Int J Syst Evol Micr 59: 3012–3018.
    [218] Sy A, Giraud E, Samba R, et al. (2001) Nodulation of certain legumes of the genus Crotalaria by the new species Methylobacterium. Can J Microbiol 47: 503–508. doi: 10.1139/cjm-47-6-503
    [219] Tiirola MA, Mannisto MK, Puhakka JA, et al. (2002) Isolation and characterization of Novosphingobium sp. strain MT1, a dominant polychlorophenol-degrading strain in a groundwater bioremediation system. Appl Environ Microbiol 68: 173–180.
    [220] Aylward FO, McDonald BR, Adams SM, et al. (2013) Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol 79: 3724–3733. doi: 10.1128/AEM.00518-13
    [221] Brady CL, Cleenwerck I, van der Westhuizen L, et al. (2012) Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus. Int J Syst Evol Micr 62: 1457–1464.
    [222] Lei X, Wang ET, Chen WF, et al. (2008) Diverse bacteria isolated from root nodules of wild Vicia species grown in temperate region of China. Arch Microbiol 190: 657–671. doi: 10.1007/s00203-008-0418-y
    [223] Mulet M, Lalucat J, Garcia-Valdes E (2010) DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12: 1513–1530.
    [224] Tripathi AK, Verma SC, Ron EZ (2002) Molecular characterization of a salt-tolerant bacterial community in the rice rhizosphere. Res Microbiol 153: 579–584. doi: 10.1016/S0923-2508(02)01371-2
    [225] Zhang Y, Qiu S (2016) Phylogenomic analysis of the genus Ralstonia based on 686 single-copy genes. Antonie Van Leeuwenhoek 109: 71–82. doi: 10.1007/s10482-015-0610-4
    [226] Brady C, Hunter G, Kirk S, et al. (2014) Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella. Syst Appl Microbiol 37: 545–552.
    [227] Ramos PL, Moreira-Filho CA, Van Trappen S, et al. (2011) An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates. Mem Inst Oswaldo Cruz 106: 394–399. doi: 10.1590/S0074-02762011000400003
    [228] Margos G, Castillo-Ramirez S, Hoen AG (2012) Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistant Staphylococcus aureus. Parasitology 139: 1952–1965. doi: 10.1017/S0031182012000741
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