Table S1. Amplification of nosZ from isolates using primers nosZ-II-F and nosZ-II-R
Organisma / Clade / Ampliconb / Annealing temperaturec(°C)
nosZ organisms:
Anaeromyxobacter dehalogens DSM-218751 / II / -
Candidatus Accumulibacter phosphatisUW-13 / II / +++ / 48-62
Desulfitobacterium hafnienseDSM-106642 / II / +, 500 / 48-51
Dyadobacter fermentansDSM-180531 / II / +++ / 48-62
Gemmatimonas aurantiacaDSM-145861 / II / +++ / 48-63
Geobacillus thermodenitrificansDSM-4651 / II / +, 500 / 48-54
Magnetospirillum magneticumAMB-11 / II / + / 51-62
Opitutus terrae DMS-112462 / II / + / 54-57,5
Pyrobaculum calidifontis JCM-115483 / II / 150, 300 / 48-58
Salinibacter ruberDSM-138552 / II / ++,650 / 48-62
Sulfurimonas denitrificansDSM-12512 / II / +, 150, 350, 500 / 48-53
Achromobacter cycloclastesATCC-219211 / I / 150, 250, 500 / 48-60
Alcaligenes faecalisATCC-87501 / I / 900 / 48-62
Paracoccus denitrificansATCC-193671 / I / -
Pseudomonas flourescensATCC 335121 / I / -
Pseudomonas stutzeriATCC-144052 / I / 400 / 48
Psychromonas ingrahamiiDSM-176642 / I / ++ 300, 800 / 49-54
Bradyrhizobium japonicumUSDA110A1 / I / -
Burkholderia thailandensisDSM-132762 / I / 150 / 48-57
Cupriavidus necatorATCC 176991 / I
Cupriavidus metalliduransATCC 431232 / I / -
Haloarcula marismortui ATCC-430493 / I / 900 / 48-51
Non-nosZ organisms:
Lactobacillus gasseri KA315-A33 / None / -
Arthrobacter chlorophenolicus A63 / None / -
aExtraction technique of genomic DNA is indicated as follows: (1) DNeasy kit (Qiagen), (2) extracted using SDS protocol, or (3) received extracted DNA from source.
bIntensity of nosZ PCR product is indicated as follows: (+) low intensity, (++) medium intensity, (+++) high intensity, or (-) for no band. Numbers indicate approximate sizes of observed non-sepcific amplification products.
cTemperature range in which PCR products where observed.
Table S2. Environmental samples for clade II nosZ clone librariesClone library / Number of Sequences / Sample / Amplicona / Site Description/Reference
Arable soil / 90 / Brunnby / ++ / Brunnby gård, Västerås, Sweden (Throbäcket al., 2004)
Logården 2 / ++ / Logården research farm, Sweden(Enwallet al., 2010)
Logården 50 / ++ / Logården research farm, Sweden(Enwallet al., 2010)
Alunda / ++ / Uppsala, Sweden (Throbäcket al., 2004)
Ulleråker / ++ / Uppsala, Sweden (Philippot et al., 2011)
Manureamended arable soil / 55 / Ram J / ++ / Ultuna, Uppsala, Sweden (Enwallet al., 2007)
PAH contaminated soil / 29 / Fin / ++ / Oil-contaminated site, Finland (Petric et al., 2011)
Rice paddy sediment / 22 / RMgM 108 / ++ / Rice-mungbean-maize paddy rotation, Vietnam (Xuan et al., 2011)
RRR 14 / + / Continuous rice paddy, TienGang, Vietnam (Xuan et al., 2011)
RRR 29 / + / Continuous rice paddy, TienGang, Vietnam (Xuan et al., 2011)
RMgM 98 / ++ / Rice-mungbean-maize paddy rotation, Vietnam (Xuan et al., 2011)
Activated sludge/ / 42 / Eskilstuna 1 / ++ / Eskilstuna, Sweden (Rodriguez-Caballero et al., 2012)
wastewater treatment plant / Eskilstuna 2 / ++ / Eskilstuna, Sweden (Rodriguez-Caballero et al., 2012)
Henriksdal B2 / +++ / Henriksdal, Stockholm, Sweden (Hallin et al., 2005)
Henriksdal B3 / +++ / Henriksdal, Stockholm, Sweden (Hallin et al., 2005)
Västerås 1 / ++ / Västerås, Sweden (Rodriguez-Caballero et al., 2012)
Västerås 2 / ++ / Västerås, Sweden (Rodriguez-Caballero et al., 2012)
Wetland / 93 / Fyris / ++ / Fyris fen, Uppsala, Sweden (unpublished)
Lake sediment / 72 / Erken littoral / ++ / Littoral sediment, lake Erken, Sweden (unpublished)
Erken limnetic / ++ / Limnetic sediment, lake Erken, Sweden (unpublished)
aIntensity of nosZ PCR product (approximately 700 bp) is indicated as follows: (+) low intensity, (++) medium intensity, (+++) high intensity, or (-) for no band.
.
Table S3.Abundance of 16S rRNA, nosZ clade I, and nosZ clade II genes in environmental samples from different habitat types based on quantitative PCR and expressed as number of gene copies per ng DNAHabitat type / Site name, Countryc / Reference / Replicates / 16S / nosZ clade I / nosZclade II
Arable Soil / Alunda, Sweden1 / (Throbäcket al., 2004) / 3 / 7.06 ± 0.42 × 105 / 8.72 ± 0.78 × 103 / 1.94 ± 0.11 × 104
Brunnby, Sweden1 / (Throbäcket al., 2004) / 3 / 4.96 ± 2.96 × 105 / 4.79 ± 2.95 × 103 / 6.54 ± 3.53 × 103
Bor, France2 / (Petric et al., 2011) / 3 / 4.47 ± 0.57 × 105 / 2.83 ± 0.49 × 103 / 2.11 ± 0.33 × 104
Mar, France2 / (Petric et al., 2011) / 3 / 5.69 ± 1.10 × 104 / 1.95 ± 0.70 × 102 / NDa
Lanna, Sweden1 / (unpublished) / 3 / 5.87 ± 0.82 × 105 / 6.89 ± 1.44 × 103 / 1.02 ± 0.16 × 104
Logården2, Sweden1 / (Enwallet al., 2010) / 3 / 4.06 ± 3.56 × 105 / 4.90 ± 4.85 × 103 / 5.87 ± 4.83 × 103
Logården50, Sweden1 / (Enwallet al., 2010) / 3 / 2.88 ± 1.34 × 105 / 2.92 ± 1.28 × 103 / 4.29 ± 1.60 × 103
EpoA, France2 / (Cheneby et al., 2010) / 3 / 1.05 ± 0.30 × 106 / 8.87 ± 2.72 × 103 / 2.63 ± 0.68 × 104
Ulleråker, France2 / (Petric et al., 2011)) / 3 / 1.03 ± 0.10 × 106 / 1.16 ± 1.04 × 104 / 1.34 ± 0.17 × 104
Bou, France2 / (Philippot et al., 2002) / 3 / 4.79 ± 0.13 × 104 / 3.93 ± 0.34 × 102 / 1.24 ± 0.17 × 103
Forest soil / Ger, Germany2 / (Petric et al., 2011) / 3 / 1.56 ± 1.42 × 106 / 8.93 ± 6.12 × 103 / 1.32 ± 1.36 × 104
Alpine soil / Himalaya 5200 m 56, Nepal / (Stres et al., 2010) / 3 / 9.52 ± 7.16 104 / 5.55 ± 3.89 × 102 / 3.33 ± 2.57 × 102
Himalaya 6000 m 66, Nepal / (Stres et al., 2010) / 3 / 2.76 ± 0.39 × 105 / 2.27 ± 0.70 × 103 / 5.74 ± 1.64 × 102
Biotechnosol / Biotechnosoil, France2 / (unpublished) / 3 / 1.01 ± 0.48 × 106 / 9.34 ± 3.95 × 103 / 1.68 ± 0.57 × 104
Rice paddy / RMgM108, Vietnam1 / (Xuan et al., 2011) / 2 / 2.71 ± 0.36 × 105 / 1.49 ± 1.73 × 103 / 1.28 ± 0.06 × 103
RRR14, Vietnam1 / (Xuan et al., 2011) / 2 / 2.30 ± 0.31 × 105 / 8.63 ± 1.28 × 102 / 7.84 ± 0.80 × 102
RRR, Vietnam1 / (Xuan et al., 2011) / 2 / 3.80 ± 1.36 × 105 / 1.35 ± 0.04 × 103 / 7.75 ± 0.59 × 102
RMgM 98, Vietnam1 / (Xuan et al., 2011) / 2 / 3.82 ± 2.23 × 105 / 2.16 ± 1.45 × 103 / 3.11 ± 2.20 × 103
Wetland / Fyris fen, Sweden1 / (unpublished) / 3 / 5.58 ± 3.56 × 105 / 6.82 ± 4.60 × 103 / 7.93 ± 4.66 × 103
Ekeby, Sweden1 / (Kjellin et al., 2007) / 3 / 3.75 ± 1.39 × 105 / 1.31 ± 0.44 × 103 / 6.02 ± 1.70 × 102
Lake sediment / Erken limnetic, Sweden1 / (unpublished) / 3 / 4.66 ± 1.43 × 105 / 3.77 ± 0.88 × 103 / 7.79 ± 1.38 × 103
Erken littoral, Sweden1 / (unpublished) / 3 / 3.81 ± 2.16 × 105 / 2.00 ± 1.09 × 103 / 4.90 ± 2.76 × 103
Composted waste / Compost, Sweden1 / (Jarvis et al., 2009) / 3 / 2.13 ± 0.64 × 106 / 6.16 ± 0.88 × 103 / 6.24 ± 2.74 × 101
Biofilm / Bartoli, Italy1 / (Granhall et al., 2010) / 3 / 9.98 ± 3.00 × 105 / 1.03 ± 0.23 × 103 / 2.59 ± 0.63 × 103
ASP WWTPb / Ekilstuna, Sweden3 / (Rodriguez-Caballero et al., 2012) / 2 / 3.14 ± 1.44 × 105 / 4.90 ± 2.96 × 103 / 4.26 ± 1.43 × 103
Västerås, Sweden3 / (Rodriguez-Caballero et al., 2012) / 2 / 5.66 ± 3.77 × 105 / 9.10 ± 6.88 × 103 / 6.43 ± 4.97 × 103
HenriksdalB2, Sweden1 / (Hallin et al., 2005) / 3 / 6.55 ± 2.27 × 105 / 6.88 ± 3.85 × 103 / 1.85 ± 0.87 × 104
HenriksdalB3, Sweden1 / (Hallin et al., 2005) / 3 / 3.18 ± 0.33 × 105 / 3.38 ± 0.41 × 103 / 7.56 ± 0.84 × 103
aNot detected, bActivated sludge process in wastewater treatment plant (municipal), cExtraction technique of genomic DNA is indicated as follows: (1) Fast DNA
Spin kit for Soil (MP Biomedical); (2) extracted using ISO protocol; (3) Qiagen kit with modified protocol for DNA extraction from Gram positive bacteria
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