Supplementary Material

Fig. S1. Neighbor-joining tree based on amino acid sequences. Branch support values of not less than 50 are dotted. The digits after the OTU name represent the total sequences from all lake sediment samples in the same OTU. The bar represents 1% sequence divergence based on the neighbor-joining algorithm.

1

2

3

4

56789

1011

12

13

14

15

Fig. S2. Results of the AdaptML model run with a pmoA maximum likelihood tree: (a)

Phylogenetic tree of all sequences, with outer and inner rings indicating seasons and lakes,

respectively. Ecotypes predicted by the model are marked at the branches. (b) The distribution of

each ecotype among seasons and between lakes.

(a)

(b)

16

17

18

19

20

21

22

23

24

25

Fig. S3. Anaerobic methane oxidation potential with sulfate and nitrate as potential electron

acceptors, respectively. The error bars indicate standard deviations.

26

27

28

29

303132

3334

Table S1. Physicochemical properties of sediment (coded with the character ‘s’) and corresponding overlying water (‘w’). Temp, ORP, TN, TP, TOC indicate the abbreviations of temperature, oxidation and reduction potential, total nitrogen, total phosphorus, and total organic carbon, respectively.

Sample wTemp

(℃)

wORP

(mV)

wpH wDO

(mg/L)

wTOC

(mg/L)

wTN

(mg/L)

wNH4+-N

(mg/L)

wNO3--N

(mg/L)

wTP

(mg/kg)

sTemp

(℃)

sORP

(mV)

spH sTOC

(g/kg)

sTN

(mg/kg)

wNH4+-N

(mg/kg)

sNO3--N

(mg/kg)

sTP

(mg/kg)

DA1 17.3 104.1 7.71 8.18 12.60 2.63 0.14 0.66 0.07 17.20 -17.50 7.37 8.17 1132.91 13.75 0.84 246.93

DA2 17.3 162.9 7.64 6.79 14.00 2.79 0.11 1.23 0.04 17.90 -13.30 7.27 7.56 1131.48 15.50 0.55 308.74

DA3 17.6 180 7.87 6.99 13.20 2.62 0.30 0.90 0.05 17.20 -11.10 7.17 6.32 966.85 14.64 2.01 305.45

DA4 17.4 137.2 7.52 6.9 11.90 2.86 0.16 0.91 0.05 17.00 -11.10 7.18 7.00 1043.11 12.08 0.75 278.26

DA5 17.8 184 7.74 7.25 12.80 2.74 0.17 1.00 0.05 17.40 -0.70 7.20 7.59 1060.49 13.32 0.87 347.42

DA6 17.9 198.9 7.91 7.37 15.00 2.42 0.14 0.96 0.06 12.60 16.30 7.21 7.38 1131.94 12.42 0.46 276.04

DB1 24.1 114.9 8.98 6.97 6.70 2.22 0.64 0.07 0.31 21.60 32.30 6.41 10.83 949.49 42.49 2.49 249.23

DB2 24.9 124.2 8.65 6.28 9.00 1.19 0.23 0.02 0.13 21.70 2.00 6.94 9.74 934.07 29.81 2.64 327.33

DB3 25.5 127.1 8.84 6.25 7.30 1.24 0.21 0.03 0.12 21.60 14.70 7.48 9.66 878.18 35.52 1.68 345.95

DB4 21.8 128.7 8.65 6.77 6.00 1.29 0.21 0.06 0.09 21.50 3.00 7.07 10.57 1001.84 28.29 2.01 316.10

DB5 22.2 143.3 8.65 6.07 9.80 1.10 0.20 0.04 0.10 21.40 -11.40 7.17 10.76 1023.15 25.45 3.17 283.75

DB6 22.5 60.9 8.56 6.67 6.90 1.22 0.65 0.02 0.09 21.50 -8.30 7.20 11.66 1122.44 37.28 1.87 403.64

DC1 9.9 159 8.33 8.66 11.20 1.90 0.25 0.13 0.12 12.40 -11.00 7.20 8.59 975.14 24.35 2.32 238.00

DC2 10.4 162.7 8.65 8.46 11.20 1.03 0.15 0.17 0.09 12.60 11.30 6.80 7.69 1106.68 38.26 0.45 344.61

DC3 11 169.5 9.02 8.47 13.30 0.90 0.27 0.16 0.12 12.60 26.40 6.60 6.38 1017.39 27.78 0.85 360.01

DC4 11.3 198.4 8.45 8.45 10.50 1.98 0.26 0.06 0.11 12.60 5.20 6.90 8.57 1037.67 31.13 1.67 290.91

DC5 11 189.7 8.98 8.39 12.20 2.50 0.28 0.07 0.11 12.30 -4.50 6.98 8.15 1069.82 23.29 1.40 328.55

DC6 10.6 192.2 8.86 8.55 13.50 1.78 0.27 0.10 0.12 12.60 16.30 6.70 8.43 957.96 28.97 1.15 360.54

EA1 14.5 223.2 8.43 7.95 13.20 0.80 0.09 0.04 0.03 14.70 -41.90 7.68 5.51 667.47 9.43 0.70 172.81

EA2 14 129.6 8.36 7.83 10.90 0.60 0.08 0.02 0.03 14.10 -31.40 7.52 6.00 806.72 12.84 0.75 161.70

353637

EA3 13.8 239.2 7.91 7.57 9.10 0.67 0.10 0.02 0.02 13.70 -50.70 7.87 6.60 810.55 13.34 1.78 158.28

EA4 15.5 157.2 8.74 7.58 9.50 0.67 0.02 0.02 0.02 15.20 -29.10 7.51 4.83 642.97 13.56 1.38 186.33

EA5 14.2 189.5 8.37 7.71 10.80 0.82 0.08 0.02 0.03 14.50 -43.80 7.74 6.02 894.10 11.19 0.68 127.59

EB1 22.5 12.6 7.92 6.12 5.60 0.63 0.31 0.02 0.02 22.50 -8.10 7.14 3.32 504.09 6.46 0.92 116.45

EB2 21 102.8 7.83 6.74 6.60 0.69 0.08 0.02 0.04 22.40 10.80 6.80 3.32 681.49 9.46 4.70 161.77

EB3 22 68.7 7.83 6.55 3.50 0.69 0.10 0.02 0.03 21.70 55.30 6.07 4.74 752.06 13.11 0.34 171.19

EB4 23.8 82.3 7.13 6.07 6.60 0.57 0.13 0.02 0.03 22.10 -18.90 7.31 4.54 682.92 9.80 1.58 172.05

EB5 24.4 95.4 7.48 5.87 7.60 0.53 0.17 0.02 0.03 21.90 -36.70 7.61 3.45 758.06 7.34 1.45 158.47

EC1 12.8 222.8 8 8.08 11.90 0.47 0.12 0.02 0.01 14.40 -35.30 7.57 6.00 838.38 19.39 1.81 159.39

EC2 13.4 176.3 8.48 8.02 14.50 0.45 0.11 0.03 0.02 14.60 -39.60 7.66 5.22 657.82 19.15 3.42 191.51

EC3 13.7 194.7 8.62 7.99 14.40 0.51 0.10 0.04 0.02 14.70 -14.50 7.29 6.74 755.49 30.74 4.11 180.05

EC4 14.1 243 7.61 7.61 12.10 0.50 0.09 0.02 0.01 14.80 -20.80 7.37 4.73 781.48 18.49 4.24 259.33

EC5 12.1 192.3 8.6 8.2 12.80 0.58 0.09 0.02 0.02 13.50 -30.70 7.47 7.05 956.32 30.46 0.63 185.47

38

Table S2. The number of OTUs and library coverage of each clone library at 0.05 and 0.07 cut-offs

Sequences OTUs CoverageSample Unique 0.05 0.07 0.05 0.07

DA1 25 6 1 1 1 1DA2 25 7 3 3 0.88 0.96DA3 25 21 7 6 0.84 0.84DA4 23 13 3 3 0.96 0.96DA5 19 12 5 4 0.67 0.94DA6 23 18 5 4 0.79 0.91DB1 25 14 4 3 0.96 1DB2 23 21 6 6 0.87 0.87DB3 25 11 3 3 1 1DB4 21 8 1 1 1 1DB5 25 9 2 2 1 1DB6 24 20 10 10 0.75 0.75DC1 24 15 3 3 1 1DC2 20 10 6 5 0.55 0.85DC3 22 20 5 4 0.95 0.95DC4 19 15 3 3 0.95 0.95DC5 20 11 4 3 0.9 0.95DC6 20 10 3 2 0.95 1EA1 25 6 1 1 1 1EA2 25 15 10 9 0.92 0.96EA3 25 10 2 2 0.96 0.96EA4 25 22 8 5 0.8 0.92EA5 20 16 6 6 0.9 0.90EB1 23 9 2 2 0.96 0.96EB2 23 19 8 6 0.57 0.87EB3 25 9 3 3 0.92 0.92EB4 24 9 1 1 1 1EB5 25 8 1 1 1 1EC1 24 11 1 1 1 1EC2 25 15 3 2 0.96 1EC3 22 11 3 3 0.95 0.95EC4 20 14 4 3 0.95 0.95EC5 21 3 1 1 1 1

7

39404142

4344