TABLE 3.
Comparative genomics of properties relevant to plant colonization and establishmenta
| Log2 fold change in abundance in the indicated group versus endophytes |
||||
|---|---|---|---|---|
| Category and feature (gene) | Symbionts | Phytopathogens | Rhizosphere bacteria | Soil bacteria |
| Chemotaxis and motility | ||||
| Aerotaxis (aer) | −0.983*** | 0.029 | −0.259 | −0.354 |
| Serine chemotaxis (tsr) | −0.697** | 0.471* | −0.284 | 0.162 |
| 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*** | 0.030 | 0.390*** | 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*** | −0.271 | 0.143 | 0.069 |
| Response regulator (cheD) | −0.206* | −0.086 | 0.040 | 0.009 |
| 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* | −0.149 | 0.045 |
| 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 | −0.034 | 0.042 |
| Stress (rstB-rstA) | −0.951*** | −0.022 | −0.005 | 0.070 |
| Carbon source utilization (creC-creB) | −0.726*** | 0.077 | −0.098 | −0.016 |
| Multidrug resistance (baeS-baeR) | −0.804*** | 0.032 | 0.074 | 0.000 |
| Copper efflux (cusS-cusR) | −0.821*** | −0.415 | 0.258 | 0.300 |
| Carbon storage regulator (barA-uvrY) | −0.989*** | −0.044 | −0.058 | 0.017 |
| 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*** | 0.038 | 0.039 | 0.180 |
| Amino sugar metabolism (glrK-glrR) | −0.974*** | −0.021 | −0.061 | 0.232 |
| Twitching motility (chpA-chpB) | −0.783*** | 0.120 | 0.026 | 0.003 |
| Extracellular polysaccharide (wspE-wspR) | −0.612*** | −0.072 | 0.044 | −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 | −0.036 | 0.068 |
| Nitric oxide reductase (norR) | −0.625*** | −0.156* | 0.193 | 0.129 |
| NAD biosynthesis (nadR) | −0.257*** | 0.012 | −0.103 | −0.079 |
| Beta-lactamase resistance (ampR) | 0.091 | 0.016 | −0.060 | −0.339*** |
| Pyrimidine metabolism (pyrR) | −0.326** | −0.051 | 0.121 | 0.015 |
| Thiamine metabolism (tenA) | 0.070 | −0.976*** | 0.109 | 0.195 |
| Stress-related enzymes | ||||
| Glutathione peroxidase (btuE) | −0.360** | −0.031 | 0.104 | −0.195 |
| Glutathione S-transferase (gst) | 0.562** | −0.435* | −0.230 | −0.351 |
| Catalase (katE) | −0.362* | −0.237 | 0.084 | 0.042 |
| Transport system | ||||
| ABC, capsular polysaccharide (kpsT) | −0.045 | −0.277*** | −0.244* | −0.221 |
| ABC, thiamine-derived products (thiY) | −0.449** | −0.958*** | 0.000 | 0.000 |
| ABC, spermidine/putrescine (potD) | 0.718*** | −0.308** | 0.092 | 0.081 |
| ABC, dipeptide (dppF) | 0.204** | −0.230*** | −0.027 | 0.09 |
| 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 | −0.096 | 0.349* | −0.266* |
| ABC, lysine/arginine/ornithine (argT) | 0.216 | −0.336 | 0.464 | −0.182 |
| ABC, l-arabinose (araG) | 0.145 | −0.067 | 0.066 | −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*** | 0.000 | 0.000 | 0.000 |
| PTS, mannose (manY) | −0.433*** | −0.287** | −0.374*** | −0.264* |
| PTS, ascorbate (sgaA) | −0.433** | 0.003 | −0.207 | 0.158 |
| PTS, phosphocarrier (furB) | −0.317* | −0.007 | −0.065 | 0.059 |
| Others, multidrug (mdtB) | 0.076 | −0.042 | −0.217** | 0.134 |
| Other, tricarboxylic (tctA) | 0.670*** | −0.018 | 0.352* | 0.481* |
| Others, C4-dicarboxylate (dctP) | −0.123 | −0.462* | 0.382* | 0.553** |
| Others, membrane pore protein (ompC) | −1.149*** | 0.090 | −0.053 | 0.071 |
| Secretion systems | ||||
| Type I RaxAB-RaxC system (raxB) | −0.270 | 0.357 | −0.234 | −0.186 |
| Type II general pathway protein (gspD) | −0.199 | 0.213 | −0.265 | 0.064 |
| Type III secretion core apparatus (yscJ) | 0.354* | 0.263** | 0.051 | −0.181** |
| Type IV conjugal DNA protein (virB2) | 0.370 | 0.125 | −0.718*** | −0.143 |
| Type VI Imp/Vas core components (hcp) | −0.360 | −0.038 | −0.045 | 0.095 |
| Twitching motility protein (pilJ) | −0.850*** | 0.058 | 0.028 | −0.002 |
| Type I pilus assembly protein (fimA) | −0.676*** | −0.300 | 0.282 | 0.158 |
| Plant growth-promoting properties | ||||
| Nitrogenase (nifH) | 0.301** | −0.676*** | 0.226 | 0.030 |
| ACC deaminase (acdS) | 0.118 | 0.223 | 0.119 | −0.344** |
| Acetoin reductase (budC) | 0.024 | −0.259*** | −0.024 | −0.059 |
| Acetolactate decarboxylase (alsD) | −1.000*** | 0.000 | 0.000 | 0.000 |
| Butanediol dehydrogenase (butB) | −0.089 | −0.090 | 0.469** | −0.319 |
| IAA biosynthesis, IAM pathway (amiE) | 0.201 | −0.067 | −0.017 | −0.029 |
| IAA biosynthesis, IPyA pathway (ipdC) | 0.077 | −0.157 | 0.291*** | −0.043 |
| IAA biosynthesis, IAN pathway (nit) | −0.156 | 0.088 | 0.084 | −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.