TABLE 2.

Copy numbers of 16S rRNA, amoA, and carbon fixation genes in genomic DNA and cDNA during and after completion of ammonia oxidation

DNACultureAOA growth phaseaGene copy no.famoA/16S rRNA gene copy no. ratio
Archaeal 16S rRNA geneBacterial 16S rRNA geneArchaeal amoANOB (Nitrospina) 16S rRNA geneCarbon fixation
4-BUDHbACCcMCEd
Genomic DNASJNH3 oxidizing1.5 × 106 (8.3 × 105)3.9 × 105 (1.8 × 105)2.9 × 106 (2.2 × 105)2.1 × 103 (9.9 × 102)1.4 × 106 (4.4 × 105)2.1 × 105 (1.2 × 104)ND2.0 × 10°
NH3 depleted8.3 × 105 (3.4 × 105)2.0 × 105 (9.4 × 104)3.3 × 106 (2.3 × 105)5.5 × 102 (2.3 × 102)1.9 × 106 (6.2 × 105)1.7 × 105 (1.1 × 104)ND3.9 × 10°
ARNH3 oxidizing6.7 × 105 (7.4 × 105)8.6 × 104 (9.2 × 104)2.7 × 105 (1.4 × 105)6.1 × 102 (1.9 × 102)7.6 × 104 (5.9 × 104)2.0 × 104 (7.9 × 103)ND0.4 × 10°
NH3 depleted1.1 × 106 (8.9 × 105)1.7 × 105 (7.8 × 104)3.1 × 106 (4.2 × 104)1.0 × 103 (5.4 × 102)2.3 × 106 (7.8 × 105)1.4 × 105 (1.4 × 104)ND2.9 × 10°
cDNASJNH3 oxidizing3.2 × 105 (2.1 × 105)4.6 × 104 (2.4 × 104)4.1 × 103 (1.3 × 103)e4.8 × 10° (1.1 × 10°)2.9 × 10° (1.4 × 10°)1.3 × 10−2
NH3 depleted3.8 × 105 (2.8 × 105)9.6 × 104 (3.0 × 104)4.5 × 101 (3.6 × 10°)2.6 × 10° (2.2 × 10°)4.5 × 10−1 (4.5 × 10−1)1.2 × 10−4
ARNH3 oxidizing5.9 × 105 (3.3 × 105)5.5 × 104 (3.3 × 104)1.0 × 104 (1.5 × 103)9.2 × 10° (4.2 × 10°)5.7 × 10° (3.1 × 10°)1.7 × 10−2
NH3 depleted4.5 × 105 (3.3 × 105)1.5 × 105 (1.5 × 105)4.4 × 101 (1.2 × 101)9.4 × 10° (2.0 × 10°)7.4 × 10−1 (9.8 × 10−1)9.8 × 10−5
  • a Cells were collected at 7 days of culture (ammonia-oxidizing phase) and at 17 days (3 days after ammonia consumption) (ammonia-depleted phase).

  • b 4-BUDH, 4-hydroxylbutyryl CoA dehydratase.

  • c ACC, acetyl-CoA carboxylase.

  • d MCE, methylmalonyl CoA epimerase; ND, not detected.

  • e —, not determined.

  • f For comparison, copy numbers of genomic DNA and cDNA were normalized based on ng of genomic DNA and total RNA, respectively. Numbers in parentheses indicate standard deviations from triplicate measurements.