Table 2.
Detection frequency of potential functional genes in the bacterial community of sugar beet taproot
| ID of KEGG | Gene lengtha | Frequency per 105 readsb | ||
|---|---|---|---|---|
|
| ||||
| ID of UniRef | length (kbp) | |||
| ACC deaminase | K01505 | UniRef50_A5EJ46 | 1.020 | 9±6 |
| IAA | 1±0.5 | |||
| tryptophan 2-monooxygenase (iaaM) | K00466 | UniRef50_A6W7Y1 | 1.707 | 0.7±0.5 |
| indolepyruvate decarboxylase (ipdC) | K04103 | UniRef50_I0BL41 | 1.755 | 0.8±0.6 |
| N2 fixationc | ND | |||
| nitrogenase iron protein (nifH) | K02588 | UniRef50_O07641 | 0.984 | ND |
| nitrogenase molybdenum-iron protein alpha chain (nifD) | K02586 | UniRef50_P19066 | 1.515 | ND |
| nitrogenase molybdenum-iron protein beta chain (nifK) | K02591 | UniRef50_P25314 | 1.566 | ND |
| nitrogenase delta subunit (anfG) | K00531 | UniRef50_O68940 | 0.351 | ND |
| PQQ biosynthesis protein (pqqC)d | UniRef50_Q6F9J1 | 0.768 | 3±0.4 | |
| Phosphate solubilization | 19±6 | |||
| quinoprotein glucose dehydrogenase (GDH) | K00117 | UniRef50_P27175 | 2.427 | 15±5 |
| 3-phytase | K01083 | UniRef50_G2IPZ8 | 1.074 | 3±2 |
| 4-phytase | K01093 | UniRef50_B0UQX3 | 1.635 | 0.3±0.4 |
| Siderophoree | 18±9 | |||
| isochorismate pyruvate lyase (pchB) | K04782 | UniRef50_Q51507 | 0.306 | 10±7 |
| nonribosomal peptide synthetase (dhbF) | K04780 | UniRef50_C6U462 | 3.270 | 3±0.6 |
| enterobactin synthetase component F (entF) | K02364 | UniRef50_P11454 | 3.882 | 1±0.6 |
| other genes | 4±3 | |||
| Plant disease suppression | 24±8 | |||
| β-1,3-glucanase | K01210 | UniRef50_R4MQJ4 | 0.885 | 18±6 |
| chitinase | K01183 | UniRef50_I4XS16 | 1.464 | 6±4 |
| Methanol utilization (Methanol dehydrogenase (MDH))f | 10±3 | |||
| undetermined MDH | UniRef90_C5ATJ3g | 1.800 | 6±0.8 | |
| xoxF gene type | UniRef90_C5ATJ3 | 1.800 | 3±2 | |
| Sucrose utilization | 7±1 | |||
| sacA | K01193 | UniRef50_P07819 | 1.440 | 6±2 |
| PTS system, sucrose-specific IIA component | M00269 | UniRef50_S6C6M4 | 1.968 | 0.6±0.9 |
| Betaine utilization | 54±8 | |||
| glycine betaine/proline transport system (proX) | K02002 | UniRef50_P0AFM3 | 0.993 | 25±3 |
| glycine betaine/proline transport system (proW) | K02001 | UniRef50_P17327 | 1.065 | 13±4 |
| glycine betaine/proline transport system (proV) | K02000 | UniRef50_P14175 | 1.203 | 16±3 |
| betaine-homocysteine S-methyltransferase | K00544 | UniRef50_A4WQF1 | 1.074 | 0.8±1 |
| N metabolism-related genesg | 296±22 | |||
| glutamine synthetase (glnA) | K01915 | UniRef50_A0R079 | 1.437 | 49±6 |
| carbonic anhydrase (cynT, can) | K01673 | UniRef50_Q9I262 | 0.663 | 40±6 |
| nitronate monooxygenase (ncd2, npd) | K00459 | UniRef50_F8GQA6 | 1.254 | 31±4 |
| glutamate dehydrogenase (gudB, rocG) | K00260 | UniRef50_B2RKJ1 | 1.338 | 26±2 |
| glutamate synthase (NADPH/NADH) small chain (gltD) | K00266 | UniRef50_P9WN18 | 1.467 | 20±3 |
| glutamate synthase (NADPH/NADH) large chain (gltB) | K00265 | UniRef50_Q05755 | 4.548 | 16±3 |
| nirnitrite reductase (NO-forming) (nirK) | K00368 | UniRef50_P81445 | 0.993 | 13±8 |
| nitrite reductase (NADH) large subunit (nirB) | K00362 | UniRef90_A6UI45 | 2.463 | 11±8 |
| other genes | 91±17 | |||
Approximately gene length (kbp) was deduced by using the information of the UniProt Reference Clusters (UniRef) database.
ND = not detected. The values represent means ± standard deviation (n=3).
nifHDK genes were not found by both MEGAN and TBLASTN search.
pqqC gene was not found by MEGAN, but found by TBLASTN search.
Top three abundant genes were shown. Other genes were grouped in the ‘other genes’ category. Full list of the genes for siderophore were shown in Table S3.
MDH gene was not found by MEGAN, but found by TBLASTN search. Type of MDH (xoxF or mxaF) was determined by the phylogenetic tree analysis (Table S2). In almost sequence reads, the MDH type could not be determined because these sequence reads located in the out group of xoxF and mxaF phylogenetic tree. Such sequence reads were shown as “undetermined MDH”.
Top eight abundant genes were shown. Other genes were grouped in the ‘other genes’ category. Full list of nitrogen metabolism related genes were shown in Table S10.
The same ID No. of UniRef as xoxF gene was used.