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. 2021 Jul 1;16(1):26–37. doi: 10.1038/s41396-021-01045-2

Table 1.

Abundances of gene and transcript reads in the metagenome (DNA) and metatranscriptome (RNA) based on RPM values.

Soil pH Time NAR NIR NOR NOSa NAR/NIR NIR/NOR NIR/NOS NOR/NOS
(h) G P G/P K S K/S Q C Q/C I II I/II

DNA

SoilA

0

146.4

(0.9)

23.9

(1.2)

6.13

(0.28)

35.6

(1.72)

0.87

(0.06)

41.2

(4.62)

69.2

(1.2)

5.7

(0.6)

12.3

(1.6)

13.1

(1.4)

5.9

(1.1)

2.3

(0.7)

4.68

(0.27)

0.49

(0.03)

1.64

(0.51)1)

3.33

(0.89)

SoilN 0

129.9

(1.6)

62.7

(1.8)

2.07

(0.05)

38.9

(1.15)

5.70

(0.36)

6.84

(0.31)

37.4

(0.8)

10.7

(0.5)

3.5

(0.2)

4.9

(0.2)

20.8

(1.6)

0.24

(0.02)

4.32

(0.12)

0.93

(0.03)

1.65

(0.26)

1.78

(0.23)

RNA 0.5 46.0 2.96 15.5 23.5 0.00 na 31.7 1.30 24.4 22.7 5.1 4.46 2.09 0.71 0.83 1.08
SoilA 0.5 45.1 1.30 34.7 23.4 0.00 na 27.3 0.70 39.0 1.98  0.84
3 104.7 2.80 37.4 40.9 0.40 102.3 98.2 1.30 75.5 42.5 8.1 5.23 2.60 0.42 0.81 1.48
3 79.9 6.60 12.1 42.1 0.00 na 52.8 0.10 528.0 2.05  0.80
SoilN 0.5 162.2 16.3 10.0 72.3 21.9 3.3 23.2 10.2 2.27 9.3 45.5 0.20 1.89 2.82 1.27 0.71
0.5 131.9 41.1 3.20 42.4 6.90 6.1 32.6 14.1 2.31 3.51  1.06
3 544.6 50.0 10.9 330.2 63.0 5.2 106.0 28.1 3.77 68.3 296.9 0.23 1.51 2.93 0.82 0.28
3 336.1 41.6 8.10 192.9 35.8 5.4 55.8 22.1 2.52 1.65  2.94
9 114.5 49.9 2.30 40.6 7.96 5.1 31.0 10.8 2.87 8.6 43.1 0.20 3.38 1.16 0.89 0.77
12 251.9 48.0 5.50 137.5 18.5 7.4 58.4 16.4 3.56 1.99  2.09
12 235.1 44.7 5.30 149.1 22.6 6.6 40.8 18.4 2.22  26.7  122.5 0.22 1.63 2.90 1.06 0.43
27 127.6 43.8 2.90 56.5 7.10 8.0 21.5 10.6 2.03 2.69  1.98
27 124.2 53.1 2.30 67.4 7.10 9.5 34.0 12.6 2.70  7.7  56.0 0.14 2.38 1.60 1.02 0.58

Results for anoxic incubation of SoilA (pH 3.8) and SoilN (pH 6.8), amended with NO3-. NAR = nitrate reductases, sum of narG and napA abundancies; NIR = nitrite reductases, sum of nirK and nirS abundancies; NOR = nitric oxide reductases, sum of qnor and cnor abundancies; NOS = nitrous oxide reductase; sum of clade I and clade II abundancies. DNA samples were taken just before the start of the incubation (t = 0 h, Fig. 1A). RNA samples were taken after 0.5 and 3 h incubation (SoilA) and after 0.5–27 h incubation (SoilN) (Fig. 1A). All values are in reads per million (RPM). Ratios of reads from selected genes/transcripts are also given. DNA: Average values are given for abundance of individual genes, values in parenthesis are standard deviation; n = 3. RNA: Duplicate metatranscriptome samples were analysed from each sampling time except for the 9 h sample from SoilN for which one samples was lost. Individual values for read abundances and ratios are shown except for the nosZ clades for which data from duplicate samples were pooled. Ratios including NOS are therefore calculated from average values.

na not applicable.

aValues were obtained using a manually curated database for nos clades containing sequences reported by Conthe et al. (2018). For this examination reads from duplicate samples in the MT were pooled before the analysis, thus replicates are not reported. Calculations of ratios were based on the same database as for the other denitrification genes, which was based on individual replicates. For detailed descriptions see Materials and Methods section.