TABLE 2.
Identification and frequency of the dominant nematode-specific DGGE bands
| DGGE type and band no. | Closest GenBank match (organism, GenBank no.)a | % identity | No. of samples where band was found |
|||||
|---|---|---|---|---|---|---|---|---|
| Nematodes |
Soil |
|||||||
| Kw | Go | Gb | Kw | Go | Gb | |||
| Fungus DGGE | ||||||||
| 1 | Malassezia restricta, EU400587 | 98.7 | 4 | 4 | 4 | 4 | 4 | 4 |
| 2 | Aspergillus penicillioides, GU017496 | 99.6 | 4 | 0 | 2 | 0 | 0 | 0 |
| 3 | Cryptococcus pseudolongus, AB105353 | 100 | 0 | 4 | 0 | 0 | 0 | 0 |
| 4 | Chaetomium globosum, JX501299 | 98.2 | 0 | 4 | 0 | 0 | 0 | 0 |
| 5 | Arthopyreniaceae, FJ439584 | 100 | 0 | 4 | 0 | 0 | 4 | 0 |
| 6 | Eurotium sp., AM901702 | 100 | 4 | 0 | 0 | 0 | 0 | 0 |
| 7 | Ganoderma applanatum, JX501311 | 99.6 | 4 | 0 | 0 | 2 | 0 | 0 |
| 8 | Cladosporinum cladosporioides, AJ300335 | 100 | 0 | 0 | 4 | 0 | 0 | 4 |
| 9 | Davidiella sp., JX164064 | 99.6 | 4 | 4 | 4 | 0 | 0 | 0 |
| 10 | Cryptococcus sp., JX164076 | 100.0 | 0 | 0 | 4 | 0 | 4 | 4 |
| 11 | Trichosporonales, EF060720 | 98.3 | 4 | 4 | 0 | 0 | 0 | 0 |
| 12 | Mortierella sp., JF439489 | 99.6 | 4 | 4 | 2 | 4 | 4 | 4 |
| 13 | Cylindrocarpon olidum, GU198183 | 99.0 | 4 | 0 | 0 | 0 | 0 | 0 |
| 14 | Ascomycete, AM410609 | 99.2 | 4 | 4 | 4 | 4 | 4 | 4 |
| 15 | Rhizophydium sp., DQ485617 | 98.7 | 4 | 4 | 2 | 0 | 0 | 0 |
| Bacillus DGGE | ||||||||
| 1 | Bradyrhizobium pachyrhizi, NR_043037 | 97.9 | 0 | 3 | 0 | 0 | 0 | 0 |
| 2 | Sphingomonas insulae, NR_044187 | 99.4 | 1 | 1 | 3 | 0 | 0 | 0 |
| 3 | Staphylococcus epidermidis, NR_036904 | 100 | 4 | 4 | 4 | 0 | 0 | 0 |
| 4 | Staphylococcus epidermidis, NR_036904 | 99.6 | 4 | 4 | 4 | 0 | 0 | 0 |
| 5 | Micrococcus endophyticus, NR_044365 | 98.6 | 3 | 3 | 4 | 0 | 0 | 0 |
| 6 | Bacillus megaterium, NR_043401 | 99.7 | 4 | 4 | 4 | 0 | 0 | 0 |
| 7 | Micrococcus luteus, NR_037113 | 99.2 | 4 | 4 | 4 | 4 | 4 | 4 |
| 8 | Propionibacterium acnes, NR_040847 | 100 | 4 | 4 | 4 | 4 | 4 | 4 |
| 9 | Methylobacterium rhodesianum, NR_041028 | 97.2 | 2 | 1 | 3 | 0 | 0 | 0 |
| 10 | Streptococcus thermophilus, NR_074827 | 100 | 0 | 0 | 3 | 0 | 0 | 0 |
| Alphaproteobacterium DGGE | ||||||||
| 1 | Solirubrobacter soli, NR_041365 | 99.8 | 2 | 3 | 1 | 3 | 3 | 0 |
| 2 | Janthinobacterium lividum, NR_026365 | 99.8 | 1 | 0 | 3 | 0 | 0 | 0 |
| 3 | Rhizobium phaseoli, NR_044112 | 99.8 | 4 | 4 | 4 | 0 | 0 | 0 |
| 4 | Pedomicrobium australicum, NR_026337 | 96.0 | 1 | 3 | 3 | 4 | 4 | 4 |
| 5 | Ochrobactrum anthropi, NR_074243 | 99.5 | 4 | 3 | 2 | 2 | 4 | 0 |
| 6 | Hyphomonadaceae, NR_041967 | 91.0 | 3 | 2 | 3 | 4 | 4 | 4 |
| 7 | Nitrospira moscoviensis, NR_029287 | 96.3 | 2 | 3 | 0 | 0 | 0 | 0 |
| 8 | Rhodobiaceae, NR_042626 | 92.8 | 2 | 2 | 2 | 0 | 0 | 0 |
| 9 | Devosia chinhatensis, NR_044214 | 96.6 | 0 | 3 | 2 | 4 | 4 | 4 |
| 10 | Kaistia soli, NR_044302 | 96.0 | 0 | 2 | 3 | 0 | 0 | 0 |
| 11 | Magnetospirillum gryphiswaldense, NR_027605 | 96.3 | 1 | 3 | 1 | 0 | 0 | 0 |
| 12 | Bosea eneae, NR_028798 | 95.5 | 4 | 4 | 4 | 0 | 0 | 0 |
| 13 | Rhodobacter blasticus, NR_043735 | 96.3 | 4 | 4 | 4 | 4 | 4 | 4 |
| Pseudomonas DGGE | ||||||||
| 1 | Pseudomonas asplenii, NR_040802 | 99.5 | 0 | 3 | 0 | 0 | 0 | 0 |
| 2 | Pseudomonas tuomuerensis, NR_043990 | 99.1 | 2 | 3 | 2 | 4 | 4 | 4 |
| 3 | Pseudomonas koreensis, NR_025228 | 100 | 3 | 0 | 0 | 0 | 0 | 0 |
| 4 | Pseudomonas jessenii, NR_024918 | 99.3 | 1 | 3 | 3 | 0 | 4 | 3 |
| 5 | Pseudomonas jessenii, NR_024918 | 99.1 | 1 | 1 | 3 | 0 | 0 | 4 |
| 6 | Pseudomonas koreensis, NR_025228 | 99.8 | 3 | 0 | 1 | 0 | 0 | 0 |
| 7 | Pseudomonas taetrolens, NR_036909 | 98.9 | 4 | 4 | 4 | 4 | 4 | 4 |
a
Details for the BLASTN results and taxonomy are given in the supplemental material. (T), type strain.