Supplemental Materials
Fig. S1 Rarefraction curves for bacterial amoA gene sequences. Clustering stringency at 97%. Note: Ha: Haliclona sp.; La: Lamellomorpha sp.; Pl: Placospongia sp.; Ac: Acanthella sp.; Ph: Pericharax heteroraphis.
Fig. S2 Rarefaction curves for archaeal amoA gene sequences. Clustering stringency at 97%. Note: Ha: Haliclona sp.; La: Lamellomorpha sp.; Sd: Spirastrellidae diplastrella; Mf: Mycale fibrexilis.
Fig. S3 Rarefaction curves for nirS gene sequences. Clustering stringency at 97%.
Note: Sd: Spirastrellidae diplastrella.
Table S1 BLAST analysis of bacterial amoA genes (The number in bracket shows the number of sequences in each OTU)
Table S2 BLAST analysis of archaeal amoA genes (The number in bracket shows the number of sequences in each OTU)
Table S3 BLAST analysis of nirS genes (The number in bracket shows the number of sequences in each OTU)
Fig. S1
Fig. S2
Fig. S3
Table S1 BLAST analysis of bacterial amoA genes
OTU / Similar sequences / Description / Source / Max identityHaAOB1(4)
JN177536 / FJ652556.1 / Uncultured ammonia-oxidizing bacterium clone ML-amoA-11 ammonia monooxygenase subunit A (amoA) gene, partial cds / USA, Florida Key Largo, sponge Mycale laxissima / 98%
HaAOB2(3)
JN177537 / EF529638.1 / Uncultured Nitrosospira sp. clone amoA-SW21 ammonia monoooxygenase subunit A (amoA) gene, partial cds / France, Banyuls sur Mer, seawater / 97%
HaAOB3(2)
JN177538 / FJ652560.1 / Uncultured ammonia-oxidizing bacterium clone IS-amoA-05 ammonia monooxygenase subunit A (amoA) gene, partial cds / USA, Florida Key Largo, sponge Ircinia strobilina / 95%
HaAOB7(5)
JN177539 / HM235899.1 / Uncultured ammonia-oxidizing bacterium isolate DGGE gel band B1 ammonium monooxygenase subunit A (amoA) gene, partial cds / China, Jiulong River estuarine sediment / 98%
DQ289944.1 / Uncultured beta proteobacterium clone LC1AG-1 amonia monooxygenase (amoA) gene, partial cds / South Atlantic Bight Permeable Shelf sediment / 98%
HaAOB14(1)
JN177540 / FJ652549.1 / Uncultured ammonia-oxidizing bacterium clone ML-amoA-01 ammonia monooxygenase subunit A (amoA) gene, partial cds / USA, Florida Key Largo, sponge Mycale laxissima / 99%
PlAOB1(5)
JN177541 / EU744330.1 / Uncultured bacterium clone YJ15 ammonium monooxygenase (amoA) gene, partial cds / China, Lake Donghu sediment / 99%
PlAOB2(5)
JN177542 / HQ202477.1 / Uncultured ammonia-oxidizing bacterium clone AOB-W-56 ammonia monooxygenase subunit A (amoA) gene, partial cds / China, Baiyangdian Lake / 99%
AcAOB1(6)
JN177543 / EU718500.1 / Uncultured bacterium clone 1 ammonia monooxygenase subunit A (amoA) gene, partial cds / Wetland / 98%
AcAOB4(2)
JN177544 / HQ247938.1 / Uncultured ammonia oxidizing bacterium clone D_25 ammonia monooxygenase subunit A (amoA) gene, partial cds / Estuarine sediment / 95%
AcAOB8(1)
JN177545 / AB373432.1 / Uncultured ammonia-oxidizing bacterium amoA gene for putative ammonia monooxygenase subunit A, partial cds, clone: OA-SA10-65 / aquarium biofilter / 99%
AcAOB9(1)
JN177546 / HM364221.1 / Uncultured bacterium clone ES-Core-VM1-sB05 ammonia monooxygenase subunit A (amoA) gene, partial cds / US, Elkhorn slough estuary sediment / 96%
PhAOB1(7)
JN177547 / GQ906697.1 / Uncultured bacterium clone NOAOB-11 ammonia-oxidizing monooxygenase subunit A (amoA) gene, partial cds / Coastal of Gulf of Mexico / 95%
PhAOB5(1)
JN177548 / AB449325.1 / Uncultured ammonia-oxidizing bacterium AmoA gene for putative ammonia monooxygenase alpha subunit, partial cds, clone: G35597 / Japan, Shizuoka, Tanoura Bay sediment / 99%
PhAOB8(1)
JN177549 / GQ906697.1 / Uncultured bacterium clone NOAOB-11 ammonia-oxidizing monooxygenase subunit A (amoA) gene, partial cds / Coastal of Gulf of Mexico / 88%
PhAOB10(1)
JN177550 / EU718500.1 / Uncultured bacterium clone 1 ammonia monooxygenase subunit A (amoA) gene, partial cds / Wetland / 97%
PhAOB11(1)
JN177551 / EF529638.1 / Uncultured Nitrosospira sp. clone amoA-SW21 ammonia monoooxygenase subunit A (amoA) gene, partial cds / France, Banyuls sur Mer, seawater / 97%
PhAOB12(2)
JN177552 / HM235906.1 / Uncultured ammonia-oxidizing bacterium isolate DGGE gel band B8 ammonium monooxygenase subunit A (amoA) gene, partial cds / China, Jiulong River estuarine sediment / 99%
PhAOB14(2)
JN177553 / AB373432.1 / Uncultured ammonia-oxidizing bacterium amoA gene for putative ammonia monooxygenase subunit A, partial cds, clone: OA-SA10-65 / aquarium biofilter / 99%
LaAOB1(4)
JN177554 / JF905796.1 / Uncultured bacterium clone 30_M13F-47_F11_1104018725J ammonia monooxygenase subunit A gene, partial cds / China, Lake Taihu sediment / 99%
LaAOB3(2)
JN177555 / AY785990.1 / Uncultured beta proteobacterium clone 509EnPA17 ammonia monooxygenase subunit A-like (amoA) gene, partial sequence / Deep-sea Endeavour hydrothermal plume / 98%
Note: The number in bracket shows the number of sequences in each OTU.
Table S2 BLAST analysis of archaeal amoA genes
OTU / Similar sequences / Description / Source / Max identityHaAOA1(2)
JN177517 / FJ601590.1 / Uncultured crenarchaeote clone MS_95G12 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, central west coast, tropical marine estuary sediment / 98%
HaAOA2(6)
JN177518 / EU049830.1 / Uncultured crenarchaeote clone LuffA10 putative ammonia monooxygenase subunit A (amoA) gene, partial cds / Australia, Queensland or Orpheus Island, sponge Luffariella sp. / 90%
HaAOA4(3)
JN177519 / FJ601562.1 / Uncultured crenarchaeote clone MS_27C4 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, central west coast, tropical marine estuary sediment / 99%
HaAOA5(1)
JN177520 / AB373387.1 / Uncultured ammonia-oxidizing archaeon amoA gene for putative ammonia monooxygenase subunit A, partial cds, clone: OA-MA-156 / aquarium biofilter / 94%
HaAOA9(1)
JN177521 / FJ601574.1 / Uncultured crenarchaeote clone MS_42B6 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, central west coast, tropical marine estuary sediment / 84%
HaAOA12(1)
JN177522 / EU049826.1 / Uncultured crenarchaeote clone CoscGrA putative ammonia monooxygenase subunit A (amoA) gene, partial cds / Australia, Queensland or Orpheus Island, sponge Coscinoderma sp. / 94%
HaAOA14(1)
JN177523 / FJ601590.1 / Uncultured crenarchaeote clone MS_95G12 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, central west coast, tropical marine estuary sediment / 98%
SdAOA1(3)
JN177524 / HM022943.1 / Uncultured crenarchaeote clone XM20-G2 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, Arabian Sea coast, water around 20m depth / 96%
SdAOA2(7)
JN177525 / HM022927.1 / Uncultured crenarchaeote clone XM20-E7 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, Arabian Sea coast, water around 20m depth / 100%
MfAOA1(7)
JN177526 / HM023032.1 / Uncultured crenarchaeote clone NM20-88F ammonia monooxygenase subunit A (amoA) gene, partial cds / India, Arabian Sea coast, water around 20m depth / 100%
MfAOA4(3)
JN177527 / HM022939.1 / Uncultured crenarchaeote clone XM20-F7 ammonia monooxygenase subunit A (amoA) gene, partial cds / India, Arabian Sea coast, water around 20m depth / 99%
LaAOA1(2)
JN177528 / EF106947.1 / Uncultured crenarchaeote clone EF500_19O12 putative ammonia monooxygenase subunit A (amoA) gene, partial cds / Monterey Bay and North Pacific subtropical gyre / 99%
LaAOA2(3)
JN177529 / GU270264.1 / Uncultured crenarchaeote clone 38H-AEA-06 ammonia monooxygenase subunit A (amoA) gene, partial cds / China, Okhotsk Sea sediment / 94%
LaAOA3(1)
JN177530 / EU049841.1 / Uncultured crenarchaeote clone SiphGrA putative ammonia monooxygenase subunit A (amoA) gene, partial cds / Australia, Bare Island, sponge Siphonochalina sp. / 99%
LaAOA5(2)
JN177531 / JF272695.1 / Uncultured archaeon clone a129.120.33d AmoA gene, partial cds / Arctic Ocean, Northern Baffin Bay, sea water column 120m depth / 100%
LaAOA7(3)
JN177532 / GU988813.1 / Uncultured crenarchaeote clone A2-34 putative ammonia monooxygenase subunit A (amoA) gene, partial cds / China, Pearl River estuary sediment / 93%
LaAOA8(1)
JN177533 / GU360762.1 / Uncultured crenarchaeote clone CCS6760_500_14 ammonia monooxygenase subunit A (amoA) gene, partial cds / Central California Current / 96%
LaAOA9(1)
JN177534 / GU360940.1 / Uncultured crenarchaeote clone CCS6760_100_16 ammonia monooxygenase subunit A (amoA) gene, partial cds / Central California Current / 96%
LaAOA11(2)
JN177535 / GQ250738.1 / Uncultured crenarchaeote clone GOM_WAOA-6 ammonia monooxygenase subunit A (amoA) gene, partial cds / Gulf of Mexico / 99%
Note: The number in bracket shows the number of sequences in each OTU.
Table S3 BLAST analysis of nirS genes
OTU / Similar sequences / Description / Source / Max identitySdnirS1(7)
JN177556 / HM438887.1 / Uncultured organism clone SD36Na33 cytochrome cd1-containing nitrite reductase (nirS) gene, partial cds / China, Hangzhou, soil / 80%
SdnirS2(3)
JN177557 / EU235830.1 / Uncultured bacterium clone S8-N-27 putative dissimilatory reductase (nirS) gene, partial cds / China, Changjiang estuary sediment / 83%
SdnirS3(13)
JN177558 / AJ248396.2 / Gamma proteobacterium D7-6 partial nirS gene for nitrite reductase, isolate D7-6 / USA, offshore Washington coast / 99%
SdnirS5(6)
JN177559 / EF558384.1 / Uncultured bacterium clone A21 dissimilatory nitrite reductase (nirS) gene, partial cds / Wetland sediment / 91%
SdnirS6(3)
JN177560 / EU236023.1 / Uncultured bacterium clone S29-N-20 putative dissimilatory reductase (nirS) gene, partial cds / China, Changjiang estuary sediment / 81%
SdnirS9(6)
JN177561 / DQ072198.1 / Uncultured bacterium clone M60-134 putative dissimilatory nitrite reductase (nirS) gene, partial cds / pelagial of the central Baltic Proper, seawater / 81%
SdnirS14(1)
JN177562 / HQ007407.1 / Uncultured bacterium clone S4-55 putative dissimilatory reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 87%
SdnirS15(2)
JN177563 / EU200544.1 / Uncultured bacterium clone H2-15 putative dissimilatory reductase (nirS) gene, partial cds / mariculture sediment / 85%
SdnirS16(1)
JN177564 / EF558384.1 / Uncultured bacterium clone A21 dissimilatory nitrite reductase (nirS) gene, partial cds / Wetland sediment / 90%
SdnirS17(1)
JN177565 / EU048462.1 / Uncultured bacterium clone C4-17 putative dissimilatory reductase (nirS) gene, partial cds / Jiaozhou Bay / 80%
SdnirS18(1)
JN177566 / GU348416.1 / Uncultured bacterium clone EPR-NS-16 dissimilatory nitrite reductase (nirS) gene, partial cds / near East Pacific Ridge hydrothermal field, deep sea sediment / 87%
SdnirS19(5)
JN177567 / EU235994.1 / Uncultured bacterium clone S18-N-31 putative dissimilatory reductase (nirS) gene, partial cds / China, Changjiang estuary sediment / 98%
SdnirS21(2)
JN177568 / EU200612.1 / Uncultured bacterium clone H4-16 putative dissimilatory reductase (nirS) gene, partial cds / mariculture sediment / 96%
SdnirS22(2)
JN177569 / HQ007494.1 / Uncultured bacterium clone S16-25 putative dissimilatory reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 86%
SdnirS24(1)
JN177570 / HM773323.1 / Uncultured bacterium clone A140205 dissimilatory nitrite reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 79%
SdnirS26(2)
JN177571 / HM773298.1 / Uncultured bacterium clone A20331 dissimilatory nitrite reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 86%
SdnirS27(2)
JN177572 / HQ007373.1 / Uncultured bacterium clone S4-21 putative dissimilatory reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 85%
SdnirS30(1)
JN177573 / EU235830.1 / Uncultured bacterium clone S8-N-27 putative dissimilatory reductase (nirS) gene, partial cds / China, Changjiang estuary sediment / 83%
SdnirS31(3)
JN177574 / EU200624.1 / Uncultured bacterium clone H4-28 putative dissimilatory reductase (nirS) gene, partial cds / mariculture sediment / 99%
SdnirS35(1)
JN177575 / HM438887.1 / Uncultured organism clone SD36Na33 cytochrome cd1-containing nitrite reductase (nirS) gene, partial cds / China, Hangzhou, soil / 78%
SdnirS36(1)
JN177576 / HQ007418.1 / Uncultured bacterium clone S9-09 putative dissimilatory reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 99%
SdnirS38(2)
JN177577 / HM773294.1 / Uncultured bacterium clone A20248 dissimilatory nitrite reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 77%
SdnirS40(1)
JN177578 / EU235771.1 / Uncultured bacterium clone S7-N-30 putative dissimilatory reductase (nirS) gene, partial cds / China, Changjiang estuary sediment / 99%
SdnirS45(1)
JN177579 / EU235830.1 / Uncultured bacterium clone S8-N-27 putative dissimilatory reductase (nirS) gene, partial cds / China, Changjiang estuary sediment / 83%
SdnirS47(1)
JN177580 / HQ007481.1 / Uncultured bacterium clone S16-11 putative dissimilatory reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 78%
SdnirS52(1)
JN177581 / HQ007478.1 / Uncultured bacterium clone S16-08 putative dissimilatory reductase (nirS) gene, partial cds / China, Pearl River estuary sediment / 99%
SdnirS54(1)
JN177582 / EU048523.1 / Uncultured bacterium clone B2-09 putative dissimilatory reductase (nirS) gene, partial cds / Jiaozhou Bay / 83%
SdnirS55(1)
JN177583 / HQ427904.1 / Uncultured bacterium clone G7-F8 putative dissimilatory reductase (nirS) gene, partial cds / China, East lake sediment / 92%
Note: The number in bracket shows the number of sequences in each OTU.
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