Table 3.
Amino acid identities of in silico translated OTU representatives of denitrification-associated genes retrieved from acidic palsa peat soil to closely related sequences
| Gene (read)b | OTU no. (accession no.) | Closest relative |
Closest cultured relative |
Relative abundance of OTUs in amplicon libraries (%) |
|||
|---|---|---|---|---|---|---|---|
| Name (accession no.) | Identity (%)a | Name (accession no.) | Identity (%)a | 0 to 20 cm | Below 20 cm | ||
| narG (forward) | 1 (HE616587) | Uncultured bacterium (AY955190) | 82 | Streptomyces coelicolor A3(2) (NC 003888) | 78 | 87.3 | 75.8 |
| 2 (HE616588) | Oligotropha carboxidovorans OM 5 (CP001196) | 84 | Oligotropha carboxidovorans OM 5 (CP001196) | 84 | 12.6 | 24.1 | |
| 3 (HE616589) | Uncultured bacterium (FJ556609) | 68 | Oceanithermus profundus DSM 14977 (CP002361) | 64 | 0.03 | 0.1 | |
| 4 (HE616590) | Rubrobacter xylanophilus DSM 9941 (CP000386) | 72 | Rubrobacter xylanophilus DSM 9941 (CP000386) | 72 | 0.07 | 0 | |
| narG (reverse) | 1 (HE616591) | Uncultured bacterium (AY955190) | 86 | Actinosynnema mirum DSM 43827 (CP001630) | 75 | 99.9 | 100 |
| 2 (HE616592) | Nitrobacter hamburgensis X14 (NC 007964) | 71 | Nitrobacter hamburgensis X14 (NC 007964) | 71 | 0.1 | 0 | |
| nirKc | 1 (HE616593) | Uncultured bacterium (DQ783977) | 97 | Bradyrhizobium sp. strain ORS278 (NC 009445) | 84 | 57.6 | 0.33 |
| 2 (HE616594) | Uncultured bacterium (EF623499) | 78 | Rhodopseudomonas palustris BisA53 (CP000463) | 76 | 12.8 | 82.9 | |
| 3 (HE616595) | Uncultured bacterium (DQ304355) | 96 | Bradyrhizobium sp. strain GSM-467 (FN600568) | 85 | 26.6 | 0.09 | |
| 4 (HE616596) | Uncultured bacterium (EU790857) | 80 | Alcaligenes sp. strain I (DQ108983) | 79 | 0 | 16.4 | |
| 5 (HE616597) | Uncultured bacterium (EU790858) | 92 | Bosea sp. MF18 (EF363545) | 92 | 2.9 | 0 | |
| 6 (HE616598) | Uncultured bacterium (DQ783907) | 82 | Bradyrhizobium sp. strain D203a (AB480454) | 76 | 0 | 0.12 | |
| 7 (HE616599) | Uncultured bacterium (DQ783888) | 85 | Bradyrhizobium sp. strain BTAi1 (NC 009485) | 81 | 0 | 0.06 | |
| 8 (HE616600) | Uncultured bacterium (EF623499) | 77 | Methylobacterium sp. strain R-25207 (AM230850) | 75 | 0 | 0.03 | |
| 9 (HE616601) | Uncultured bacterium (EU790858) | 79 | Rhizobium etli CFN 42 (NC 007766) | 78 | 0 | 0.03 | |
| nirSd | 1 (HE616602) | Uncultured bacterium (GQ443982) | 92 | Rubrivivax gelatinosus (AB536930) | 80 | 0 | 36.2 |
| 2 (HE616603) | Uncultured bacterium (GU393200) | 86 | Pseudomonas sp. strain I-Bh25-14 (FN555560) | 75 | 0 | 31.6 | |
| 3 (HE616604) | Uncultured bacterium (GU393229) | 87 | Bradyrhizobium sp. strain TSA26 (AB542313) | 84 | 86.3 | 8.5 | |
| 4 (HE616605) | Uncultured bacterium (GU393213) | 88 | Thiobacillus denitrificans ATCC 25259 (CP000116) | 76 | 0 | 9.0 | |
| 5 (HE616606) | Uncultured bacterium (HM438800) | 95 | Dechlorospirillum sp. strain I-Bh37-22 (FN555562) | 80 | 0 | 5.3 | |
| 6 (HE616607) | Uncultured bacterium (DQ676123) | 85 | Thiobacillus denitrificans ATCC 25259 (CP000116) | 80 | 0 | 4.6 | |
| 7 (HE616608) | Uncultured bacterium (DQ676123) | 84 | Aromatoleum aromaticum EbN1 (NC 006513) | 78 | 0 | 3.1 | |
| 8 (HE616609) | Uncultured bacterium (GU393183) | 78 | Cupriavidus sp. strain TSA25 (AB542312) | 74 | 0 | 0.84 | |
| 9 (HE616610) | Uncultured bacterium (GU393076) | 92 | Bradyrhizobium sp. strain TSA1 (AB542304) | 86 | 6.3 | 0 | |
| 10 (HE616611) | Uncultured bacterium (GU393229) | 87 | Rhodanobacter sp. strain D206a (AB480490) | 85 | 5.0 | 0.12 | |
| 11 (HE616612) | Uncultured bacterium (AY583422) | 89 | Cupriavidus metallidurans CH34 (CP000352) | 77 | 0 | 0.48 | |
| 12 (HE616613) | Uncultured bacterium (GU393076) | 94 | Bradyrhizobium sp. strain TSA1 (AB542304) | 87 | 2.5 | 0 | |
| 13 (HE616614) | Uncultured bacterium (DQ303103) | 84 | Rhodanobacter sp. strain D206a (AB480490) | 82 | 0 | 0.12 | |
| 14 (HE616615) | Uncultured bacterium (DQ676123) | 82 | Cupriavidus sp. strain N24 (AB480486) | 78 | 0 | 0.12 | |
| nosZ (forward) | 1 (HE616616) | Uncultured bacterium (FN430557) | 96 | Oligotropha carboxidovorans OM 5 (CP001196) | 85 | 51.1 | 51.9 |
| 2 (HE616617) | Uncultured bacterium (FN430533) | 91 | Burkholderia pseudomallei K96243 (BX571965) | 90 | 43.4 | 37.6 | |
| 3 (HE616618) | Uncultured bacterium (FN430550) | 87 | Pseudomonas brassicacearum PD 5 (DQ377777) | 82 | 3.8 | 8.1 | |
| 4 (HE616619) | Alcaligenes faecalis A15 (AF361795) | 95 | Alcaligenes faecalis A15 (AF361795) | 95 | 1.5 | 1.0 | |
| 5 (HE616620) | Azospirillum sp. TSO41-3 (AB545691) | 83 | Azospirillum sp. strain TSO41-3 (AB545691) | 83 | 0 | 1.2 | |
| 6 (HE616621) | Uncultured bacterium (FN430537) | 90 | Azospirillum brasilense SpT60 DSM 2298 (AF361792) | 90 | 0.06 | 0 | |
| 7 (HE616622) | Uncultured bacterium (FN430542) | 89 | Burkholderia pseudomallei K96243 (BX571965) | 87 | 0 | 0.1 | |
| nosZ (reverse) | 1 (HE616623) | Uncultured bacterium (FN430557) | 95 | Rhodopseudomonas palustris HaA2 (CP000250) | 81 | 52.3 | 52.1 |
| 2 (HE616624) | Uncultured bacterium (FN430533) | 91 | Azospirillum lipoferum (AF361793) | 85 | 42.4 | 36.5 | |
| 3 (HE616625) | Uncultured bacterium (FN430533) | 87 | Mesorhizobium sp. strain TSA41b (AB542285) | 79 | 4.7 | 10.0 | |
| 4 (HE616626) | Ralstonia solanacearum GMI1000 (AL646053) | 85 | Ralstonia solanacearum GMI1000 (AL646053) | 85 | 0.59 | 0.36 | |
| 5 (HE616627) | Uncultured bacterium (FJ209438) | 83 | Mesorhizobium sp. strain D246 (AB480521) | 76 | 0 | 0.94 | |
| 6 (HE616628) | Bradyrhizobium japonicum USDA 110 (BA000040) | 88 | Bradyrhizobium japonicum USDA 110 (BA000040) | 88 | 0 | 0.07 | |
a
Determined after alignment in MEGA, version 5.0.
b
Where indicated, analyses were based on forward or reverse reads.
c
Analyses included forward and reverse complements of reverse reads; minimal sequence overlaps of forward and reverse reads were 130 bases.
d
Analyses included forward and reverse complements of reverse reads; minimal sequence overlaps of forward and reverse reads were 190 bases.