TABLE 1

Descriptions, primers, and references for each target functional gene

Gene(s)General functionSpecific functionPrimer namePrimer sequenceReference
C cycling
    cbbL-RCO2 fixationLarge subunit of form I red-like RubisCOcbbLR1FAAGGAYGACGAGAACATC60
cbbLR1intRTGCAGSATCATGTCRTT
    SDIMO genesHydrocarbon degradationAlpha subunit of soluble di-iron monooxygenases; oxidizes diverse hydrocarbons, including common urban pollutants like propene and vinyl chlorideNVC66CCANCCNGGRTAYTTRTTYTCRAACCA8
NVC57CAGTCNGAYGARKCSCGNCAYAT
    bphAPCB degradationBiphenyl dioxygenase; aerobic degradation of PCBS, a priority urban pollutantbphAf668-3GTTCCGTGTAACTGGAARTWYGC61
bphAr1153-2CCAGTTCTCGCCRTCRTCYTGHTC
N cycling
    tfdAPhenoxy herbicide degradationOxoglutarate dioxygenase; degrades phenolic acids found in many herbicidesTfdA421dFACSGARTTCKSIGACATGC62
TfdA778vkRAGCGGTTGTCCCACATCAC
    nosZDenitrificationSubunit of nitrous oxide reductase; catalyzes reduction of N2O to N2nosZ2FCGCRACGGCAASAAGGTSMSSGT63
nosZ2RCAKRTGCAKSGCRTGGCAGAA
    amoANitrificationActive site of ammonia monooxygenases; oxidizes ammoniaA189GNGACTGGGACTTCTGG64
amoA-2RCCCCTCKGSAAAGCCTTCTTC
S cycling
    apsASulfur oxidation and carbon fixationAdenosine phosphosulfate; oxidizes sulfur to sulfateapsAFTGGCAGATMATGATYMACGG65
apsARGGGCCGTAACCGTCCTTGAA