76. Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26: 1362-1384.

77. Udwary DW, Gontang EA, Jones AC, Jones GS, Schultz AW, 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.

78. Velázquez-Robeldo R, Contreras-Cornejo H, Macías-Rodriguez LI, Hernández-Morales A, Aguirre J, et al. (2011) Role of the 4-phosphopantetheinyl transferase of *Trichoderma virens* in secondary metabolism, and induction of plant defense responses. Mol Plant Microb Interact 24: 1459-1471.

79. Mukherjee PK, Buensanteai N, Moran-Diez ME, Druzhinina IS, Kenerley CM (2012) Functional analysis of non-ribosomal peptide synthetases (NRPs) in *Trichoderma virens* reveals a polyketide synthase (PKS)/NRPS hybrid enzyme involved in the induced systemic resistance response in maize. Microbiol 158: 155-165.

80. Tornus D, Floss HG (2001) Identification of four genes from the granaticin biosynthetic gene cluster of Strepomyces violaceoruber Tü22 involved in the biosynthesis of L-rhodisone. J Antibiot 54: 91-101.

81. Tadra-Sfeir MZ, Souza EM, Faoro H, Müller-Santos M, Baura VA, et al. (2011) Naringenin regulates expression of genes involved in cell wall synthesis in *Herbaspirillum seropedicae* Appl Environ Microbiol 77: 2180-2183.

82. Abdel-Lateif K, Boguz D, Hocher V (2012) The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and *Frankia* bacteria. Plant Signal Behav 7: 636-641.

83. Hammad Y, Nalin R, Marechal J, Fiasson K, Pepin R, et al. (2003) A possible role for phenyl acetic acid (PAA) on *Alnus glutinosa* nodulation by *Frankia* bacteria. Plant and Soil 254: 193-206.

84. Duca D, Lorz J, Patten CL, Rose D, Glick BR (2014) Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 106: 85-125.

85. Spaepen S, Vanderleyden J, Remans R (2007) Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 31: 425-448.

86. Kobayashi M, Izui H, Nagasawa T, Yamada H (1993) Nitrilase in biosynthesis of the plant hormone indole-3-acetic acid from indole-3-acetonitrile: cloning of the *Alcaligenes* gene and site-directed mutagenesis of cysteine residues. Proc Natl Acad Sci 90: 247-251.

87. Kobayashi M, Suzuki T, Fujita T, Masuda M, Shimizu S (1995) Occurrence of enzymes involved in biosynthesis of indole-3-acetic acid from indole-3-acetonitrile in plant-associated bacteria, *Agrobacterium* and *Rhizobium*. Proc Natl Acad Sci 92: 714-718.

88. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, et al. (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci 100: 4927-4933.

89. Ochman H, Wilson AC (1987) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26: 74-86.

90. Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms re-revisited. Amer J Bot 97: 1-8.

91. Zakhia F, Jeder H, Willems A, Gillis M, Dreyfus B, et al. (2006) Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Microb Ecol 51: 375-393.

92. Gtari M, Ghodhbane-Gtari F, Nououi I, Beauchemin N, Tisa LS (2012) Phylogenetic perspectives of nitrogen-fixing actinobacteria. Arch Microbiol 194: 3-11.

93. Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, et al. (2011) Genome of *Herbaspirillum seropedicae* strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 7: e1002064. doi:10.1371/journal.pgen.1002064.

94. Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, et al. (2011) *Azospirillum* genomes reveal transition of bacteria from aquatic to terrestrial environments. Plos Genetics 7: e1002430. doi: 10.1371/journal.pgen.1002430.

95. Medie FM, Davies GJ, Drancourt M, Henrissat B (2012) Genome analyses highlight the different biological roles of cellulases. Nat Rev Microbiol 10: 227-234.

96. Alonso-Vega P, Normand P, Bacigalupe R, Pujic P, Lajus A, et al. (2012) Genome sequence of *Micromonospora lupini* Lupac 08, isolated from root nodules of *Lupinus angustifolius*. J Bacteriol 194: 4135.

97. Vallenet D, Labarre L, Rouy Z, Barbe C, Bocs S, et al. (2006) MaGe-a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34: 53-65.

98. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.

99. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.

100. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.

101. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 20: 2731-2739.

102. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147. doi: 10.1371/journal.pone.0011147.

103. Blom J, Albaum S, Doppmeier D, Pühler A, Vorhölter FJ, et al. (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10: 154. doi: 10.1186/1471-2105-10-154.

104. Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the *Salmonella* pathogenicity islands. Bioinformatics 22: 2196-2203.

105. Vicente-Villardón JL (2010) MULTIBIPLOT: A package for Multivariate Analysis using Biplots. Departamento de Estadística. Universidad de Salamanca. Available: http://biplot.usal.es/ClassicalBiplot/index.html.

106. Ren Q, Chen K, Paulsen IT (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35: 274-279.

107. Rowbotham TJ, Cross T (1977) Ecology of *Rhodococcus coprophilus* and associated actinomycetes in fresh water and agricultural habitats. J Gen Microbiol 100: 231-240.

108. Mateos PF, Jimenez-Zurdo JI, Chen J, Squartini AS, Haack SK, et al. (1992) Cell-associated pectinolytic and cellulolytic enzymes in *Rhizobium leguminosarum* biovar trifolii. Appl Environ Microbiol 58: 1816-1822.

109. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, et al. (1983) Numerical classification of *Streptomyces* and related genera. J Gen Microbiol 129: 1743-1813.

110. Murthy N, Bleakley B (2012) Simplified method of preparing colloidal chitin used for screening of chitinase-producing microorganisms. Internet J Microbiol 10: DOI:10.5580/2bc3.

111. Milagres AMF, Machuca A, Napoleão D (1999) Detection of siderophore production from several fungi and bacteria by a modification of chrome azurol S (CAS) agar plate assay. J Microbiol Meth 37: 1-6.

112. Glickmann E, Dessaux Y (1995) A critical examination of the specificity of the salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61: 793-796.

113. Gordon SA, Weber RP (1951) Colorimetric estimation of indole acetic acid. Plant Physiol 26: 192-195.

114. Rigaud J, Puppo A (1975) Indole-3-acetic acid catabolism by soybean bacteroids. J Gen Microbiol 88: 223-228.

115. Hardy RWF, Hoilsten RD, Jackson EK, Burns RC (1968) The acetylene-ethylene assay for N₂ fixation: laboratory and field evaluation. Plant Physiol 43: 1185-1207.
76. Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26: 1362-1384.

77. Udwary DW, Gontang EA, Jones AC, Jones GS, Schultz AW, 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.

78. Velázquez-Robeldo R, Contreras-Cornejo H, Macías-Rodriguez LI, Hernández-Morales A, Aguirre J, et al. (2011) Role of the 4-phosphopantetheinyl transferase of *Trichoderma virens* in secondary metabolism, and induction of plant defense responses. Mol Plant Microb Interact 24: 1459-1471.

79. Mukherjee PK, Buensanteai N, Moran-Diez ME, Druzhinina IS, Kenerley CM (2012) Functional analysis of non-ribosomal peptide synthetases (NRPs) in *Trichoderma virens* reveals a polyketide synthase (PKS)/NRPS hybrid enzyme involved in the induced systemic resistance response in maize. Microbiol 158: 155-165.

80. Tornus D, Floss HG (2001) Identification of four genes from the granaticin biosynthetic gene cluster of Strepomyces violaceoruber Tü22 involved in the biosynthesis of L-rhodisone. J Antibiot 54: 91-101.

81. Tadra-Sfeir MZ, Souza EM, Faoro H, Müller-Santos M, Baura VA, et al. (2011) Naringenin regulates expression of genes involved in cell wall synthesis in *Herbaspirillum seropedicae* Appl Environ Microbiol 77: 2180-2183.

82. Abdel-Lateif K, Boguz D, Hocher V (2012) The role of flavonoids in the establishment of plant roots endosymbioses with arbuscular mycorrhiza fungi, rhizobia and *Frankia* bacteria. Plant Signal Behav 7: 636-641.

83. Hammad Y, Nalin R, Marechal J, Fiasson K, Pepin R, et al. (2003) A possible role for phenyl acetic acid (PAA) on *Alnus glutinosa* nodulation by *Frankia* bacteria. Plant and Soil 254: 193-206.

84. Duca D, Lorz J, Patten CL, Rose D, Glick BR (2014) Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 106: 85-125.

85. Spaepen S, Vanderleyden J, Remans R (2007) Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev 31: 425-448.

86. Kobayashi M, Izui H, Nagasawa T, Yamada H (1993) Nitrilase in biosynthesis of the plant hormone indole-3-acetic acid from indole-3-acetonitrile: cloning of the *Alcaligenes* gene and site-directed mutagenesis of cysteine residues. Proc Natl Acad Sci 90: 247-251.

87. Kobayashi M, Suzuki T, Fujita T, Masuda M, Shimizu S (1995) Occurrence of enzymes involved in biosynthesis of indole-3-acetic acid from indole-3-acetonitrile in plant-associated bacteria, *Agrobacterium* and *Rhizobium*. Proc Natl Acad Sci 92: 714-718.

88. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, et al. (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci 100: 4927-4933.

89. Ochman H, Wilson AC (1987) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26: 74-86.

90. Bell CD, Soltis DE, Soltis PS (2010) The age and diversification of the angiosperms re-revisited. Amer J Bot 97: 1-8.

91. Zakhia F, Jeder H, Willems A, Gillis M, Dreyfus B, et al. (2006) Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya. Microb Ecol 51: 375-393.

92. Gtari M, Ghodhbane-Gtari F, Nououi I, Beauchemin N, Tisa LS (2012) Phylogenetic perspectives of nitrogen-fixing actinobacteria. Arch Microbiol 194: 3-11.

93. Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, et al. (2011) Genome of *Herbaspirillum seropedicae* strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 7: e1002064. doi:10.1371/journal.pgen.1002064.

94. Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, et al. (2011) *Azospirillum* genomes reveal transition of bacteria from aquatic to terrestrial environments. Plos Genetics 7: e1002430. doi: 10.1371/journal.pgen.1002430.

95. Medie FM, Davies GJ, Drancourt M, Henrissat B (2012) Genome analyses highlight the different biological roles of cellulases. Nat Rev Microbiol 10: 227-234.

96. Alonso-Vega P, Normand P, Bacigalupe R, Pujic P, Lajus A, et al. (2012) Genome sequence of *Micromonospora lupini* Lupac 08, isolated from root nodules of *Lupinus angustifolius*. J Bacteriol 194: 4135.

97. Vallenet D, Labarre L, Rouy Z, Barbe C, Bocs S, et al. (2006) MaGe-a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34: 53-65.

98. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.

99. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.

100. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.

101. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 20: 2731-2739.

102. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147. doi: 10.1371/journal.pone.0011147.

103. Blom J, Albaum S, Doppmeier D, Pühler A, Vorhölter FJ, et al. (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10: 154. doi: 10.1186/1471-2105-10-154.

104. Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the *Salmonella* pathogenicity islands. Bioinformatics 22: 2196-2203.

105. Vicente-Villardón JL (2010) MULTIBPLOT: A package for Multivariate Analysis using Biplots. Departamento de Estadística. Universidad de Salamanca. Available: http://biplot.usal.es/ClassicalBiplot/index.html.

106. Ren Q, Chen K, Paulsen IT (2007) TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res 35: 274-279.

107. Rowbotham TJ, Cross T (1977) Ecology of *Rhodococcus coprophilus* and associated actinomycetes in fresh water and agricultural habitats. J Gen Microbiol 100: 231-240.

108. Mateos PF, Jimenez-Zurdo JI, Chen J, Squartini AS, Haack SK, et al. (1992) Cell-associated pectinolytic and cellulolytic enzymes in *Rhizobium leguminosarum* biovar trifolii. Appl Environ Microbiol 58: 1816-1822.

109. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, et al. (1983) Numerical classification of *Streptomyces* and related genera. J Gen Microbiol 129: 1743-1813.

110. Murthy N, Bleakley B (2012) Simplified method of preparing colloidal chitin used for screening of chitinase-producing microorganisms. Internet J Microbiol 10: DOI:10.5580/2bc3.

111. Milagres AMF, Machuca A, Napoleão D (1999) Detection of siderophore production from several fungi and bacteria by a modification of chrome azurol S (CAS) agar plate assay. J Microbiol Meth 37: 1-6.

112. Glickmann E, Dessaux Y (1995) A critical examination of the specificity of the salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61: 793-796.

113. Gordon SA, Weber RP (1951) Colorimetric estimation of indole acetic acid. Plant Physiol 26: 192-195.

114. Rigaud J, Puppo A (1975) Indole-3-acetic acid catabolism by soybean bacteroids. J Gen Microbiol 88: 223-228.

115. Hardy RWF, Hoilsten RD, Jackson EK, Burns RC (1968) The acetylene-ethylene assay for N₂ fixation: laboratory and field evaluation. Plant Physiol 43: 1185-1207.