TABLE 1.
Phylotypes of nifH associated with switchgrass
| Phylotype | Closest relative | Accession no. | Similarity (%) | No. of sequences per sample type |
Taxonomic description | |||
|---|---|---|---|---|---|---|---|---|
| Root |
Shoot DNA | Total | ||||||
| DNA | RNA | |||||||
| OTU-01 | Bradyrhizobium sp. strain BTAi 1 | BAC07281 | 98–100 | 35 | 0 | 15 | 50 | Alphaproteobacteria |
| OTU-02 | Bradyrhizobium sp. strain MAFF 210318 | BAC07283 | 94–98 | 46 | 2 | 71 | 119 | Alphaproteobacteria |
| OTU-03 | Mesorhizobium loti | BAF95636 | 100 | 0 | 0 | 4 | 4 | Alphaproteobacteria |
| OTU-04 | Methylocystis sp. strain LW2 | AAK97418 | 97–98 | 24 | 2 | 8 | 34 | Alphaproteobacteria |
| OTU-05 | Burkholderia sp. strain WSM3937 | ABX80637 | 93–98 | 58 | 17 | 1 | 76 | Betaproteobacteria |
| OTU-06 | Burkholderia sp. strain JPY105 | AFM28513 | 97 | 7 | 7 | 3 | 17 | Betaproteobacteria |
| OTU-07 | Burkholderia sp. strain PTK47 | AAU85620 | 96–100 | 3 | 0 | 20 | 23 | Betaproteobacteria |
| OTU-08 | Sphingomonas azotifigens | BAE71134 | 95–99 | 81 | 0 | 55 | 136 | Alphaproteobacteria |
| OTU-09 | Novosphingobium sp. strain Rr 2-17 | ZP_10360790 | 98–99 | 29 | 0 | 0 | 29 | Alphaproteobacteria |
| OTU-10 | Bradyrhizobium japonicum | ACT67985 | 92–98 | 71 | 0 | 2 | 73 | Alphaproteobacteria |
| OTU-11 | Rubrivivax gelatinosus | BAE15985 | 90–94 | 0 | 5 | 0 | 5 | Betaproteobacteria |
| OTU-12 | Methylobacterium nodulans | AAQ82902 | 94–97 | 6 | 38 | 4 | 48 | Alphaproteobacteria |
| OTU-13 | Amorphomonas oryzae | BAF48338 | 96 | 0 | 1 | 7 | 8 | Alphaproteobacteria |
| OTU-14 | Rhizobium helanshanense | ADP37388 | 95–100 | 0 | 88 | 40 | 128 | Alphaproteobacteria |
| OTU-15 | Sinorhizobium sp. strain SCAU224 | AFH96094 | 98 | 3 | 0 | 1 | 4 | Alphaproteobacteria |
| OTU-16 | Azospirillum lipoferum | ABG88868 | 96–100 | 3 | 2 | 22 | 27 | Alphaproteobacteria |
| OTU-17 | Methylomonas sp. strain MG30 | CCH22595 | 93 | 5 | 0 | 0 | 5 | Gammaproteobacteria |
| OTU-18 | Pseudomonas stutzeri | CAC03734 | 97 | 7 | 4 | 0 | 11 | Gammaproteobacteria |
| OTU-19 | Klebsiella sp. strain AL060224_04 | ACM68399 | 99–100 | 0 | 0 | 18 | 18 | Gammaproteobacteria |
| OTU-20 | Azoarcus sp. strain BH72 | YP_932042 | 96–98 | 1 | 21 | 0 | 22 | Betaproteobacteria |
| OTU-21 | Desulfuromonas acetoxidans | ZP_01312343 | 94–99 | 0 | 32 | 31 | 63 | Deltaproteobacteria |
| OTU-22 | Anaeromyxobacter sp. strain Fw109-5 | YP_001380211 | 93–97 | 12 | 0 | 15 | 27 | Deltaproteobacteria |
| OTU-23 | Geobacter uraniireducens Rf4 | YP_001229952 | 92 | 1 | 0 | 5 | 6 | Deltaproteobacteria |
| OTU-24 | Geobacter sp. strain M21 | YP_003021955 | 93–96 | 4 | 3 | 0 | 7 | Deltaproteobacteria |
| OTU-25 | Geobacter sp. strain M21 | YP_003021955 | 97–98 | 35 | 15 | 5 | 55 | Deltaproteobacteria |
| OTU-26 | Geobacter uraniireducens Rf4 | YP_001229952 | 95–97 | 3 | 0 | 6 | 9 | Deltaproteobacteria |
| OTU-27 | Anaeromyxobacter sp. strain Fw109-5 | YP_001380211 | 88–91 | 0 | 5 | 2 | 7 | Deltaproteobacteria |
| OTU-28 | Desulfotomaculum gibsoniae | ZP_09101754 | 93–95 | 0 | 0 | 15 | 15 | Firmicutes |
| OTU-29 | Geobacter sp. strain M21 | YP_003021955 | 89–92 | 13 | 0 | 0 | 13 | Deltaproteobacteria |
| OTU-30 | Desulfovibrio magneticus RS-1 | YP_002953433 | 89 | 4 | 0 | 0 | 4 | Deltaproteobacteria |
| OTU-31 | Syntrophobacter fumaroxidans | YP_845148 | 90–93 | 0 | 0 | 16 | 16 | Deltaproteobacteria |
| OTU-32 | Methylocystis sp. strain LW5 | AAK97419 | 98 | 2 | 0 | 0 | 2 | Alphaproteobacteria |
| OTU-33 | Coraliomargarita akajimensis | YP_003550022 | 89 | 1 | 0 | 1 | 2 | Verrucomicrobia |
| OTU-34 | Cupriavidus sp. strain pp2.75 | ADM25241 | 92 | 1 | 0 | 0 | 1 | Betaproteobacteria |
| OTU-35 | Rhizobium sp. strain SMF 466_6 | CCN27451 | 98 | 0 | 0 | 2 | 2 | Alphaproteobacteria |
| OTU-36 | Paenibacillus graminis | BAH23271 | 94 | 0 | 0 | 2 | 2 | Firmicutes |
| OTU-37 | Rhizobium sp. strain SMF 466_6 | CCN27451 | 92 | 0 | 2 | 0 | 2 | Alphaproteobacteria |
| OTU-38 | Nostoc sp. strain PCC 7120 | NP_484917 | 99 | 0 | 0 | 2 | 2 | Cyanobacteria |
| OTU-39 | Calothrix sp. strain LEGE 06100 | AGG40738 | 97 | 0 | 0 | 1 | 1 | Cyanobacteria |
| OTU-40 | Ectothiorhodospira haloalkaliphila | ABN10975 | 88 | 1 | 0 | 0 | 1 | Gammaproteobacteria |
| OTU-41 | Desulfatibacillum alkenivorans | YP_002430688 | 93 | 1 | 0 | 0 | 1 | Deltaproteobacteria |
| OTU-42 | Bradyrhizobium sp. strain cmy11 | AEP33459 | 96 | 1 | 0 | 0 | 1 | Alphaproteobacteria |
| OTU-43 | Rhizobium sp. strain SMF 466_6 | CCN27451 | 97 | 0 | 0 | 1 | 1 | Alphaproteobacteria |
| OTU-44 | Cupriavidus sp. strain pp2.75 | ADM25241 | 98 | 1 | 0 | 0 | 1 | Betaproteobacteria |
| OTU-45 | Dechloromonas aromatica | YP_284634 | 98 | 1 | 0 | 0 | 1 | Betaproteobacteria |
| OTU-46 | Ectothiorhodospira haloalkaliphila | ABN10975 | 90 | 1 | 0 | 0 | 1 | Gammaproteobacteria |
| OTU-47 | Heliorestis baculata | BAD80875 | 88 | 0 | 1 | 0 | 1 | Firmicutes |
| OTU-48 | Mesorhizobium tianshanense | CAR57837 | 96 | 0 | 0 | 1 | 1 | Alphaproteobacteria |
| OTU-49 | Methylocystis echinoides | AAO49390 | 89 | 1 | 0 | 0 | 1 | Alphaproteobacteria |
| OTU-50 | Pelobacter carbinolicus | YP_006717849 | 93 | 0 | 0 | 1 | 1 | Deltaproteobacteria |
| OTU-51 | Geobacter bemidjiensis | YP_002138883 | 95 | 1 | 0 | 0 | 1 | Deltaproteobacteria |
| OTU-52 | Halorhodospira halophila | ABN10970 | 94 | 0 | 1 | 0 | 1 | Gammaproteobacteria |