Table S1. The tested 72 target genes in this study

Gene Predicte N Gene Gene Forward categor Encoded protein d length Forward sequence (5' → 3') Reverse primer Reverse sequence (5' → 3') o. function name primer y (bp)

starch 1 amyA α-amylase 316 AmyA-F YGGTTTTCGTCTTGACGCSG AmyA-R MGGCTGMGTRTCATGRTTK hydrolysis

starch 2 amyX pullulanase 365 AmyX-F TATAAYTGGGGMTATGAYCC AmyX-R CCCATYAAATCAAAWCGRAA hydrolysis

starch 3 apu amylopullulanase 287 Apu-F ACVTGGATAGGYGAGCCYCA Apu-R CCRTCSGGGAAGTAGTTKCC hydrolysis

starch 4 iso-plu Isopullulanase 540 Ipu-F GTCATYTACTTYGGNCC Ipu-R CGNGCSACATCNGCCCA hydrolysis

starch 5 sga glucoamylase 375 Sga-F CGSAACTGGGAYTACCGS Sga-R TCCCACAGSCCSKCGTC hydrolysis

C hemi-cellulos α-L-arabinofuranosidas 6 abfA 349 AbfA-F CGSTAYCCSGGCGGCAAYTT AbfA-R TGCCASGGNCCGTCCATYTC cycling e hydrolysis e

hemi-cellulos 7 manB β- mannanase 323 ManB-F ATGCGCGGBGTCAACCA ManB-R TCGTTGSCGATGTTGABGA e hydrolysis

hemi-cellulos 8 xylA xylose isomerase 464 XylA-F TGGGGBGGTCGYGAAGG XylA-R ACTTTGGCRTCRAAGTT e hydrolysis

cellulose cellobiose 9 cdh 130 Cdh-F ATWRYCTWCCGMRTHGCCMT Cdh-R GTKAGSGGRTTBYKGRYCAT hydrolysis dehydrogenase

cellulose 10 cex exoglucanase 380 Cex-F YSTACGGSATGCACTGGMT Cex-R TANCGCAGRTAGTCVCCCAT hydrolysis

cellulose α-N-acetylglucosamini 11 naglu 217 Naglu-F TVAAYTGGTAYCTGAAATAY Naglu-R CCRTGYAGVGCCATCCAGTC hydrolysis dase pectin pectinase/polygalactur 12 pgu 380 Pgu-F ANCATTGGTGGCCSTGGAA Pgu-R TTRAYGGCRATRCARTCRTC hydrolysis onase

chitin 13 chiA endochitinase 300 ChiA-F TSAAGAARTACGCSGACAACG ChiA-R ASGTCATCAGRCCCTTSAG hydrolysis

chitin 14 exo-chi exochitinase 400-430 ExoChi-F GATTGGTSVCAATATGAYRG ExoChi-R STCCARCCACCRAYRCTRAA hydrolysis

lignin 15 glx glyoxal oxidase 312 Glx-F AACCAGTCGATCATCTACGA Glx-R RTGSACGAGCTCDGGCATGG hydrolysis

lignin 16 lig lignin peroxidase 243 Lig-F CCGCACACACTGTTGCTGC Lig-R CGAAGGATTGCCACTCGCA hydrolysis

lignin 17 mnp manganese peroxidase 294 MnP-F MACRCCSTTCGACTCSACC MnP-R ACGTCSGAGCAGTCRAYGA hydrolysis

lignin 18 pox phenol oxidase 155 Pox-F ACYAGTATCCATTGGCACGGT Pox-R AGATGVGARTGATACCARAA hydrolysis

acetyl-CoA carboxylase

19 C fixation accA carboxyltransferase α 284 AccA-F GAAGGCTAYCGCAARGC AccA-R CCTTCMGGSGARATMAC

subunit

ATP-citrate lyase β 20 C fixation aclB 333 892F TGGACMATGGTDGCYGGKGGT 1204R ATAGTTKGGSCCACCTCTTC subunit

acetyl-coenzyme A 21 C fixation acsA 331 AcsA-F GATACCTGGTGGCAGACCGA AcsA-R TGATCACGTCGTCGACCCGG synthetase

acetyl-CoA synthase 22 C fixation acsB 420 ACSF1 CTYTGYCAGTCMTTYGCBCC ACSR1 CCCATAAABCCYGGDGTYTG complex β subunit

5-methyltetrahydrofola

23 C fixation acsE te corrinoid 331 acsE-F TCATCGGCGAACGCATCAAC acsE-R AGRCCGGCTTCSATGGC

methyltransferase carbohydrate diacid

24 C fixation cdaR regulon transcriptional 433 CdaR-F CGARATGGTGGTGCTCAA CdaR-R CARCGTRTTACGATGAATA

regulator

fumarate reductase 25 C fixation frdA 302 FrdA-F MTGCTGCACACSCTGTW FrdA-R CCGGTSGGGTGRWACTG flavoprotein subunit

2-oxoglutarate

ferredoxin 26 C fixation korA 252 KorA-F GCCGGCTACCCCATCACCCC KorA-R ATGATGGGATGGTCGCCATG oxidoreductase α

subunit

mesaconyl-CoA C1-C4 27 C fixation mct 320 Mct-F TGGGCGCSGASGTSATMCG Mct-R TTGACSGTRTARTCSAYSGC CoA transferase

methyl-coenzyme M GGTGGTGTMGGDTTCACMCART 28 C fixation mcrA 450 McrA-F McrA-R CGTTCATBGCGTAGTTVGGRTAGT reductase α subunit A

acetyl/propionyl-CoA 29 C fixation pccA 413 PccA-F GTGMTGATCAAGGCCWC PccA-R CGSGTGTTCATYTCSAGGAA carboxylase alpha

ribulose-bisphosphate 30 C fixation rbcL 272 rbbLR1F AAGGAYGACGAGAACATC rbbLR1intR TGCAGSATCATGTCRTT carboxylase large chain

succinyl-CoA:(S)- 31 C fixation smtA 340 SmtA-F TTTCTGGCCGGBTAYGCDGC SmtA-R CGGTACGGHCCGGTYTGVCC malate CoA transferase

methane quinoprotein glucose 32 gcd 300 Gcd-F ATCGCGTTCGGGCCGGACG Gcd-R ATSAGRTTSAGCTCGTCCCA production dehydrogenase

methanol

methane dehydrogenase 33 mxaF 560 f1003 GCGGCACCAACTGGGGCTGGT r1561 GGGCAGCATGAAGGGCTCCC production (cytochrome c) subunit

1

34 methane mmoX methane 350 MmoX-F ATGGAGGCGGTCAAGGACGA MmoX-R CGCTTCATGCCCTTCCACAG oxidation monooxygenase

component A alpha

chain

methane/ammonia methane 35 pmoA monooxygenase 531 A189 GGNGACTGGGACTTCTGG A682 GAASGCNGAGAAGAASGC oxidation subunit A

nitrogenase iron AAAGGYGGWATCGGYAARTCCA 36 N fixation nifH 400 nifHF nifHRb TGSGCYTTGTCYTCRCGGATBGGCAT protein CCAC

ammonia

37 Nitrification amoA1 monooxygenase α 635 Arch-amoAF STAATGGTCTGGCTTAGACG Arch-amoAR GCGGCCATCCATCTGTATGT

subunit (Archaea)

ammonia

38 Nitrification amoA2 monooxygenase α 490 amoA-1F GGGGTTTCTACTGGTGGT amoA-2R CCCCTCKGSAAAGCCTTCTT

subunit (Bacteria)

ammonia

39 N Nitrification amoB monooxygenase β 501 amoBMf TGGTAYGACATKAWATGG amoBMr RCGSGGCARGAACATSGG

cycling subunit

hydroxylamine 40 Nitrification hao 218 TGTCACATGGGTGTAGACCA ACCTGGAACATACCCAT oxidoreductase

nitrite oxidoreductase 41 Nitrification nxrA 322 F1370-F1 CAGACCGACGTGTGCGAAAG F2843-R2 TCCACAAGGAACGGAAGGTC α subunit

Denitrificatio nitrate reductase α 42 narG 110 1960m2F TAYGTSGGGCAGGARAAACTG 2050m2R CGTAGAAGAAGCTGGTGCTGT n chain

Denitrificatio nitrite reductase 43 nirK1 514 nirK1F GGMATGGTKCCSTGGCA nirK5R GCCTCGATCAGRTTRTGGTT n (NO-forming)

44 Denitrificatio nirK2 nitrite reductase 450 nirKC1F ATGGCGCCATCATGGTNYTNCC nirKC1R TCGAAGGCCTCGATNARRTTRTG n (NO-forming)

Denitrificatio nitrite reductase TGCACATCGCCAACGGNATGTW 45 nirK3 400 nirKC2F nirKC2R GGCGCGGAAGATGSHRTGRTCNAC n (NO-forming) YGG

Denitrificatio nitrite reductase 46 nirS1 425 nirScd3AF GTSAACGTSAAGGARACSGG nirSR3cd GASTTCGGRTGSGTCTTGA n (NO-forming)

Denitrificatio nitrite reductase ATCGTCAACGTCAARGARACVG 47 nirS2 400 nirSC1F nirSC1R TTCGGGTGCGTCTTSABGAASAG n (NO-forming) G

Denitrificatio nitrite reductase TGGAGAACGCCGGNCARGTNTG 48 nirS3 400 nirSC2F nirSC2R GATGATGTCCACGGCNACRTANGG n (NO-forming) G

Denitrificatio 49 nosZ1 nitrous-oxide reductase 267 nosZ2F CGCRACGGCAASAAGGTSMSSGT nosZ2R CAKRTGCAKSGCRTGGCAGAA n

Denitrificatio 50 nosZ2 nitrous-oxide reductase 454 nosZ-F CGYTGTTCMTCGACAGCCAG nosZ1622R CGSACCTTSTTGCCSTYGCG n

Ammonificat 51 ureC urease 340 ureC-F AAGMTSCACGAGGACTGGGG ureC-R AGRTGGTGGCASACCATSAGCAT ion

Anaerobic GACATACCCATACTKGTRTANACNG 52 ammonium hzo hydrazine oxidase 224 HzoQPCR1F AAGACNTGYCAYTGGGGWAAA HzoQPCR1R T oxidation

Anaerobic hydrazine synthase α 53 ammonium hzsA 260 hzsA_1597F WTYGGKTATCARTATGTAG hzsA_1857R AAABGGYGAATCATARTGGC subunit oxidation

Anaerobic hydrazine synthase β 54 ammonium hzsB 381 HSBeta296F ARGGHTGGGGHAGYTGGAAG HSBeta742R GTYCCHACRTCATGVGTCTG subunit oxidation

Assimilatory assimilatory nitrate 55 nasA 750-800 nas964 CARCCNAAYGCNATGGG nasA1735 ATNGTRTGCCAYTGRTC N reduction reductase catalytic subunit

Dissimilatory periplasmic nitrate 56 napA 490 napAf1 CTGGACIATGGGYTTIAACCA napAr1 CCTTCYTTYTCIACCCACAT N reduction reductase

Organic N glutamate 57 mineralizatio gdhA 240 GdhA-F GCCATCGGYCCWTACAAGGG GdhA-R ATGTCRCCNGCCGGAACGTC dehydrogenase n

P GACGCAGCCGAYGAYCCNGCNI 58 mineralizatio bpp β-propeller phytase 160-200 BPP-F BPP-R CAGGSCGCANRTCIACRTTRTT TNTGG n

P ruminal cysteine GTGGACCTRCGRMARGARWCIC GTCCGACCATTGCCTGCYTCRCARTG 59 mineralizatio cphy 380-400 Cphy-F Cphy-R phytase A RAMRTGIADCCA n

P phosphonate transport

60 mineralizatio phnK system ATP-binding 366 PhnK-F CATCGTCGGCGAATCCGG PhnK-R TGCTGCATGCCGCCGGAAAA

n protein

P P

61 cycling mineralizatio phoD alkaline phosphatase D 370 ALPS-F730 CAGTGGGACGACCACGAGGT ALPS-R1101 GAGGCCGATCGGCATGTCG

n

P alkaline

62 mineralizatio phoX phosphatase/Pho 600 phoX2-F GARGAGAACWTCCACGGYTA phoX2-R GATCTCGATGATRTGRCCRAAG

n regulon

methanol/ethanol P pqq-md 63 family PQQ-dependent 293 Mdh-F TGTTCTATGTGCCGGCCAA Mdh-R CTTCCACAGTTCCTTGCC solubilization h dehydrogenase

P pyrroloquinoline-quino 64 pqqC 300 PqqC-F AACCGCTTCTACTACCAG PqqC-R GCGAACAGCTCGGTCAG solubilization ne synthase P 65 ppk polyphosphate kinase 296 Ppk-F GACCCGAABGTRCTBGCSAT Ppk-R TTATAATTNCCSGTNCCNA biosynthesis

66 P hydrolysis ppx exopolyphosphatase 310 Ppx-F TGCATCTGGCGGACGGCCT Ppx-R AGATCCGCCGCCAATATCA

adenosine-5’-phosphos

67 S reduction apsA ulfate reductase α 279 APS7-F GGGYCTKTCCGCYATCAAYAC RH2-aps-R ATCATGATCTGCCAGCGGCCGGA

subunit

sulfite reductase α 68 S reduction dsrA 222 DSR1F ACSCACTGGAAGCACG RH3-dsr-R GGTGGAGCCGTGCATGTT S subunit

cycling sulfite reductase β 69 S reduction dsrB 390 DSRp2060F CAACATCGTYCAYACCCAGGG DSR4R GTGTAGCAGTTACCGCA subunit

sulfur-oxidizing 70 S oxidation soxY 329 SoxY-F ATCGATGACAACCCCGTGCC SoxY-R AGCTGGTCCATCTGCATGCCG protein

71 S oxidation yedZ sulfite oxidase 291 YedZ-F CTGCTGATCACGCTGGCCAT YedZ-R GCGATGCAGCTTCTTCCAGCG

ribosomal RNA gene Referen Reference 16S 72 sequence (reference 393 F515 GTGCCAGCMGCCGCGG R907 CCGTCAATTCMTTTRAGTTT ce gene gene rRNA gene)

Table S2. Absolute abundance of 72 genes under aCO2 and eCO2

Gene abundance

gene function(gene number) Gene name (copies×107 g-1 soil)

aCO2 eCO2 Significance

C cycling

amyA – 1.29 ± 1.12

amyX – –

starch hydrolysis(5) apu 1.75 ± 0.22 2.8 ± 0.53 * iso-plu – –

sga 8.04 ± 2.27 9.94 ± 0.91

abfA 7.63 ± 2.08 9.21 ± 1.24 hemi-cellulose hydrolysis (3) manB 3.99 ± 3.46 6.89 ± 0.58

xylA 7.18 ± 1.83 8.79 ± 1.11

cdh – –

cellulose hydrolysis (3) cex 5.35 ± 1.3 6.61 ± 1.28 ** naglu – –

pectin hydrolysis (1) pgu 0.77 ± 1.12 2 ± 0.31

chiA 2.46 ± 0.72 3.31 ± 0.15 chitin hydrolysis (2) exo-chi – –

glx 2.08 ± 0.82 3.34 ± 0.21

lig 3 ± 0.45 4.28 ± 1.03 lignin hydrolysis (4) mnp 5.14 ± 1.41 7.09 ± 1.53 ** pox – –

accA 3.04 ± 1.27 3.43 ± 0.37

C fixation (13) aclB 3.64 ± 0.95 4.68 ± 0.99 ** acsA 8.68 ± 2.52 10.67 ± 1.06

acsB – –

acsE 6.98 ± 1.94 8.8 ± 0.84

cdaR – –

frdA 5.01 ± 1.76 6.42 ± 0.36

korA 5.05 ± 1.47 6.52 ± 0.81

mct 5.31 ± 1.68 6.86 ± 0.75

mcrA – –

pccA 3.27 ± 1.12 4.24 ± 0.44

rbcL 6.38 ± 1.85 7.66 ± 0.8

smtA 7.66 ± 1.94 9.47 ± 1.21

gcd 5.94 ± 1.81 7.43 ± 0.68 methane production (2) mxaF 4.3 ± 1.26 5.3 ± 0.71

mmoX 4.63 ± 1.22 5.96 ± 0.78 * methane oxidation (2) pmoA 1.6 ± 0.25 3.04 ± 0.34 * N cycling

N fixation (1) nifH 3.74 ± 0.96 5.18 ± 0.51 * amoA1 1.57 ± 1.42 2.45 ± 2.15

amoA2 3.43 ± 1.57 3.55 ± 0.31

Nitrification (5) amoB 0.92 ± 0.8 –

hao – –

nxrA 4.43 ± 1.45 5.03 ± 0.56

narG 1.57 ± 0.77 2.23 ± 0.42

nirK1 3.69 ± 1.32 5.28 ± 0.37

Denitrification (9) nirK2 1.39 ± 1.52 2.88 ± 1.11

nirK3 6.35 ± 2.37 7.73 ± 1.07

nirS1 4.2 ± 1.54 5.24 ± 0.59

nirS2 3.06 ± 0.99 3.78 ± 0.77

nirS3 3.54 ± 1.14 4.49 ± 0.12

nosZ1 4.15 ± 1.63 5.4 ± 0.55

nosZ2 6.65 ± 1.74 8.4 ± 1.1 * Ammonification (1) ureC 7.94 ± 2.25 9.82 ± 1.13

hzo – –

Anaerobic ammonium oxidation (3) hzsA – –

hzsB – 1.74 ± 0.5 * Assimilatory N reduction (1) nasA – –

Dissimilatory N reduction (1) napA 4.17 ± 1.76 4.79 ± 0.22

Organic N mineralization (1) gdhA 5.46 ± 1.51 6.77 ± 0.9

P cycling

bpp – 0.87 ± 0.41

cphy – –

P mineralization (5) phnK 7.87 ± 2.06 9.92 ± 0.97

phoD 6.53 ± 1.65 8.18 ± 1.07 * phoX 2.88 ± 1.64 2.63 ± 1.32

pqq-mdh 5.63 ± 1.4 7.04 ± 1.17 * P solubilization (2) pqqC 4.54 ± 1.19 6.08 ± 0.84 * P biosynthesis (1) ppk – –

P hydrolysis (1) ppx 7.43 ± 1.78 9.36 ± 1.42 * S cycling

apsA 4.73 ± 1.8 6.12 ± 0.39

S reduction (3) dsrA 1.25 ± 0.26 2.36 ± 0.36 ** dsrB – –

S oxidation (2) soxY 6.75 ± 2.06 8.24 ± 0.55

yedZ 7.1 ± 1.75 8.96 ± 1.32 * Reference gene 16S rRNA 11.02 ± 2.77 13.37 ± 1.55 P<0.05, *; P<0.01, **.

Figure Figure S1 .

Relative PLFAsmain ofabundance 32 underaCO

Relative abundances of 32 main PLFAs under aCO 2 and eCO2 /% 25 10 15 20 0 5

14:0 15:0 16:0 * eCO aCO 17:0 *

18:0 2 2 a14:0 a15:0 15:0 DMA i15:0 10-Me-16:0 * a16:0 i16:0 16:1 ω5c 16:1 ω7c 16:1 ω7c DMA 16:1 ω9c * 2

10-Me-17:0 and eCO and a17:0 * 17:0 cyclo ω7c * i17:0 * 2 17:1 iso ω9c . 32 PLFAs . 32 were n=3,analyzed,P<0.05, 10-Me-17:1 ω7c 17:1 ω8c * 10-Me-18:0 i18:0 18:1 ω7c * 10-Me-18:1 ω7c

18:1 ω8c * 18:1 ω9c * 18:2 ω6,9c

19:0 cyclo ω7c * 19:1 ω8c *

*.