Table 2 Genome characteristics of AOB isolates from acidic tea soil.
Characteristic | TNL100 | TNL200 | TNL300 | N. multiformis ATCC25196 | TNE100 | N. eutropha C91 |
|---|---|---|---|---|---|---|
Genome size (bp) | 3,219,516 | 3,311,969 | 3,220,272 | 2,487,704 | 3,234,309 | 2,812,094 |
GC bases (%) | 53.6 | 55.9 | 53.7 | 48.3 | 53.9 | 50.7 |
CDSs | 3082 | 3063 | 3074 | 2,876 | 2448 | 2462 |
rRNA genes (5 S, 16 S, 23 S) | 1,1,1 | 1,1,1 | 1,1,1 | 1,1,1 | 1,1,1 | 1,1,1 |
tRNA | 43 | 43 | 43 | 41 | 43 | 41 |
Ammonia monooxygenase (amoCAB) | (TNL_08690- TNL_08710, TNL_24540- TNL_24560, TNL_29830- TNL_29850) | (TNV_05500-TNV_05520, TNV_23300-TNV_23320, TNV_30100-TNV_30120) | (TNS_08670 -TNS_08690, TNS_24540 -TNS_24560, TNS_29800 - TNS_29820) | 2 copies (Nmul_2326 − 2324, Nmul_a0798-800) | (TNE_19190-TNE_19170, TNE_21250-TNE_21230) | 2 copies (Neut_2078 − 2076) |
amoC (singleton) | (TNL_02230, TNL_03820, TNL_10530, TNL_30390) | (TNV_01100) | (TNS_02220, TNS_03810, TNS_10520, TNS_30590) | 2 (Nmul_A0177, Nmul_A2467) | (TNE_13570) | 1 (Neut_1520) |
amoD (singleton) | (TNL_24520, TNL_29810) | (TNV_05540, TNV_30080) | (TNS_24520, TNS_29780) | 1 (Nmul_2322) | (TNE_19150, TNE_21210) | 2 (Neut_2074, Neut_2315) |
amoE (singleton) | (TNL_24530, TNL_29820) | (TNV_05530, TNV_30090) | (TNS_24530, TNS_29790) | 1 (Nmul_2323) | (TNE_19160, TNE_21220) | 2 (Neut_2075, Neut_2316) |
Ammonium transporter | (TNL_05390) | (TNV_27770) | (TNS_05370) | 1 copy (Nmul_A0516) | 0 | 0 |
Hydroxylamine oxidoreductase (haoAB) | (TNL_08750-TNL_08760, TNL_11610-TNL_11620, TNL_28620-TNL_28630 | (TNV_21470-TNV_21480, TNV_23250-TNV_23260, TNV_28840-TNV_28850) | (TNS_08730-TNS_08740, TNS_11600-TNS_11610, TNS_28590-TNS_28600) | 3 (Nmul_A0805-804, Nmul_A1082-1083, Nmul_A2662-2661) | (TNE_15140- TNE_15150, TNE_16300- TNE_16310, TNE_21410- TNE_21420) | 3 (Neut_1672 − 1671, Neut_1793 − 1792, Neut_2335 − 2334) |
Cytochrome c554 (cycA) | (TNL_08740, TNL_11630, TNL_28610) | (TNV_21460, TNV_23270, TNV_28830) | (TNS_08720, TNS_11620, TNS_28580) | 3 (Nmul_A0803, Nmul_A1084, Nmul_A2660) | (TNE_15130, TNE_16290, TNE_21400) | 3 (Neut_1670, Neut_1791, Neut_2333) |
Cytochrome cM552 (cycB) | (TNL_08730, TNL_11640, TNL_28600) | (TNV_21450, TNV_23280, TNV_28820) | (TNS_08710, TNS_11630, TNS_28570) | 3 (Nmul_A0802, Nmul_A1085, Nmul_A2659) | (TNE_16280, TNE_21390) | 2 (Neut_1790, Neut_2332) |
Nitrosocyanin | (TNL_17110) | (TNV_13740) | (TNS_17110) | 1 (Nmul_A1601) | (TNE_20160) | 1 (Neut_2173) |
Nitrite reductase (nirK) | (TNL_21400) | (TNV_02220, TNV_28860) | (TNS_21420) | 1 (Nmul_A1998) | (TNE_12860) | 1 Neut_1403) |
Nitric oxide reductase (norCBQD) | 0 | 0 | 0 | 1 copy (Nmul_A1256- A1253) | norCBQD (TNE_04180- TNE_04150) norQ (TNE_06930) | 1 copy (Neut_0518–0521) |
Heme-copper Nitric oxide reductase (sNOR; norSY-norSenC) | (TNL_28650-TNL_28680) | 0 | (TNS_28620-TNS_28650) | 1 copy (Nmul_A2667- A2664) | (TNE_17140- TNE_17170) | 1 copy (Neut_1874–1876) |
Cytochrome c’-beta (cytS) | (TNL_03610) | (TNV_03900) | (TNS_03600) | 1 copy (Nmul_A2484) | (TNE_12240) | 1 copy (Neut_0132) |
Cytochrome P460 (cytL) | 0 | 0 | 0 | 0 | (TNE_00120) | 1 copy (Neut_0132) |
Cytochrome C552 | TNL_26390 | TNV_27980 | TNS_26400 | 1 copy (Nmul_A0802) | (TNE_20670) | 0 |
Plasmid | 2 | 1 | 1 | 2 | 2 | 0 |
Urease operon (ureABC, ureD, ureEFG) | (TNL_13260 - TNL_13320) | (TNV_28580 - TNV_28640) | (TNS_13270 - TNS_13330) | (Nmul_A1238- A1245) | 0 | 0 |
Urea transporter | TNL_13330 | TNV_28570 | TNS_13340 | Nmul_A1245 | 0 | 0 |
Genome GenBank accession | AP041000 | AP041003 | AP041005 | GCA_000196355.1 | AP040997 | GCA_000014765.1 |
Plasmid ID and GenBank accession | pTNL100a: AP041001 pTNL100b: AP041002 | pTNL200: AP041004 | pTNL300: AP041006 | – | pTNE100a: AP040998 pTNE100b: AP040999 | – |
Origin | Tea field soil | Tea field soil | Tea field soil | Soil | Tea field soil | Sewage |
Reference | This study | This study | This study | This study |
