TABLE 3

Comparative genomics of properties relevant to plant colonization and establishmenta

Category and feature (gene)Log2 fold change in abundance in the indicated group versus endophytes
SymbiontsPhytopathogensRhizosphere bacteriaSoil bacteria
Chemotaxis and motility
    Aerotaxis (aer)−0.983***0.029−0.259−0.354
    Serine chemotaxis (tsr)−0.697**0.471*−0.2840.162
    Aspartate/maltose chemotaxis (tar)−0.315−0.262−0.276*−0.041
    Ribose chemotaxis (rbsB)1.076***−0.423−0.108−0.252
    Galactose chemotaxis (mglB)−0.257***0.0300.390***0.283**
    Dipeptide chemotaxis (tap)−0.174**−0.172−0.215***−0.089
    Response regulators (cheBR)−0.276−0.519***−0.153−0.280*
    Response regulator (cheV)−0.880***−0.2710.1430.069
    Response regulator (cheD)−0.206*−0.0860.0400.009
    Response regulator (cheC)−0.367*−0.861***0.096−0.298
    Response regulator (cheZ)−0.271−0.202−0.396***−0.155
    Flagellar apparatus (fliI)−0.252**−0.201*−0.1490.045
    Chemotaxis and motility (motA)−0.555***−0.297*0.094−0.065
Signal transduction—two-component systems
    Magnesium assimilation (phoQ-phoP)−0.951***0.052−0.0340.042
    Stress (rstB-rstA)−0.951***−0.022−0.0050.070
    Carbon source utilization (creC-creB)−0.726***0.077−0.098−0.016
    Multidrug resistance (baeS-baeR)−0.804***0.0320.0740.000
    Copper efflux (cusS-cusR)−0.821***−0.4150.2580.300
    Carbon storage regulator (barA-uvrY)−0.989***−0.044−0.0580.017
    Antibiotic resistance (evgS-evgA)−0.868***−0.522***0.143−0.288
    Nitrogen fixation/metabolism (ntrY-ntrX)−0.037−0.233***−0.615***−0.089
    Type IV fimbria synthesis (pilS-pilR)−0.902***0.0380.0390.180
    Amino sugar metabolism (glrK-glrR)−0.974***−0.021−0.0610.232
    Twitching motility (chpA-chpB)−0.783***0.1200.0260.003
    Extracellular polysaccharide (wspE-wspR)−0.612***−0.0720.044−0.023
    Cell fate control (pleC-pleD)−0.131***−0.255**−0.639***0.094
    Redox response (regB-regA)−0.004−0.204*−0.099−0.136
Transcriptional regulators
    Nitrogen assimilation (nifA)−0.133−0.757***−0.359***−0.220
    Carbon storage regulator (sdiA)0.617***−0.067−0.055−0.279*
    Biofilm formation (crp)−0.976***0.036−0.0360.068
    Nitric oxide reductase (norR)−0.625***−0.156*0.1930.129
    NAD biosynthesis (nadR)−0.257***0.012−0.103−0.079
    Beta-lactamase resistance (ampR)0.0910.016−0.060−0.339***
    Pyrimidine metabolism (pyrR)−0.326**−0.0510.1210.015
    Thiamine metabolism (tenA)0.070−0.976***0.1090.195
Stress-related enzymes
    Glutathione peroxidase (btuE)−0.360**−0.0310.104−0.195
    Glutathione S-transferase (gst)0.562**−0.435*−0.230−0.351
    Catalase (katE)−0.362*−0.2370.0840.042
Transport system
    ABC, capsular polysaccharide (kpsT)−0.045−0.277***−0.244*−0.221
    ABC, thiamine-derived products (thiY)−0.449**−0.958***0.0000.000
    ABC, spermidine/putrescine (potD)0.718***−0.308**0.0920.081
    ABC, dipeptide (dppF)0.204**−0.230***−0.0270.09
    ABC, branched-chain amino acid (livK)0.571−0.884**−0.629−0.734
    ABC, cystine (fliY)−0.28−0.270*0.225−0.355*
    ABC, methionine (metN)−0.478***−0.336*0.031−0.163
    ABC, histidine (hisJ)−0.302−0.0960.349*−0.266*
    ABC, lysine/arginine/ornithine (argT)0.216−0.3360.464−0.182
    ABC, l-arabinose (araG)0.145−0.0670.066−0.342***
    ABC, rhamnose (rhaT)−0.129−0.826***−0.043−0.724***
    PTS, cellobiose (celB)−1.425***−0.947***−0.073−0.146
    PTS, glucose (ptsG)−0.860***0.0000.0000.000
    PTS, mannose (manY)−0.433***−0.287**−0.374***−0.264*
    PTS, ascorbate (sgaA)−0.433**0.003−0.2070.158
    PTS, phosphocarrier (furB)−0.317*−0.007−0.0650.059
    Others, multidrug (mdtB)0.076−0.042−0.217**0.134
    Other, tricarboxylic (tctA)0.670***−0.0180.352*0.481*
    Others, C4-dicarboxylate (dctP)−0.123−0.462*0.382*0.553**
    Others, membrane pore protein (ompC)−1.149***0.090−0.0530.071
Secretion systems
    Type I RaxAB-RaxC system (raxB)−0.2700.357−0.234−0.186
    Type II general pathway protein (gspD)−0.1990.213−0.2650.064
    Type III secretion core apparatus (yscJ)0.354*0.263**0.051−0.181**
    Type IV conjugal DNA protein (virB2)0.3700.125−0.718***−0.143
    Type VI Imp/Vas core components (hcp)−0.360−0.038−0.0450.095
    Twitching motility protein (pilJ)−0.850***0.0580.028−0.002
    Type I pilus assembly protein (fimA)−0.676***−0.3000.2820.158
Plant growth-promoting properties
    Nitrogenase (nifH)0.301**−0.676***0.2260.030
    ACC deaminase (acdS)0.1180.2230.119−0.344**
    Acetoin reductase (budC)0.024−0.259***−0.024−0.059
    Acetolactate decarboxylase (alsD)−1.000***0.0000.0000.000
    Butanediol dehydrogenase (butB)−0.089−0.0900.469**−0.319
    IAA biosynthesis, IAM pathway (amiE)0.201−0.067−0.017−0.029
    IAA biosynthesis, IPyA pathway (ipdC)0.077−0.1570.291***−0.043
    IAA biosynthesis, IAN pathway (nit)−0.1560.0880.084−0.019
    IAA biosynthesis, IAN pathway (nthAB)−0.136−1.054***−0.596***−0.147
  • a The relative abundances of the assigned functional properties in each investigated group (symbionts [n = 42], phytopathogens [n = 29], rhizosphere bacteria [n = 42], or soil bacteria [n = 49]) compared to endophytes (n = 40) are shown as normalized log2 fold changes. Negative values are shown if the endophyte group has a higher abundance. Significant changes were computed with a zero-inflated Gaussian mixture model, and the alpha levels, denoted by *, **, and ***, were assigned to q-value thresholds of 0.05, 0.01, and 0.001, respectively.