. 2019 Oct 21;9:15068. doi: 10.1038/s41598-019-51584-0

Table 1.

Specification of primers applied for the detection of different functional genes related to autotrophic prokaryotes based on ddPCR.

Pathway, Targeted protein, Phylogenetic coverage	Primer Name	Sequence (5′-3′)	Pconc^a	Ta^b	Reference
CBB-cycle
RubisCO form IA	cbbL_IA_f	CGGCACSTGGACCACSGTSTGGAC	200	59	Alfreider et al.⁴³
Proteobacteria (α, β, γ), Actinobacteria, Cyanobacteria	cbbL_IA_r	GTARTCGTGCATGATGATSGG	200	59	Alfreider et al.⁴³
RubisCO form IA in chemoautotrophs	cbbL_IA_CHEM	GARGGNTCNGTNGTYAACGT	400	58	Alfreider & Bogensperger³⁰
Proteobacteria (α, β, γ), Actinobacteria	cbbL_IA_r	GTARTCGTGCATGATGATSGG	400	58	Alfreider & Bogensperger³⁰
RubisCO form IC	cbbLR1F	GAACATCAAYTCKCAGCCCTT	200	57	Alfreider et al.³⁴
Proteobacteria (α, β, γ), Actinobacteria	cbbLR1R	TGGTGCATCTGVCCGGCRTG	200	57	Alfreider et al.³⁴
RubisCO form IC dominant in lakes	cbbL_IC_lake_f	AGCCGTMARYAAAGCCAGC	200	60	This study
Burkholderiales	cbbL_IC_lake_r	CGTARAARCCSCGGATCATC	200	60	This study
RubisCO form II	cbbM_f	GGCACCATCATCAAGCCCAAG	200	53	Alfreider et al.⁴³
Proteobacteria (α, β, γ), Dinophyceae	cbbM_r	TCTTGCCGTAGCCCATGGTGC	200	53	Alfreider et al.⁴³
3-HP/4-HB cycle
4-hydroxybutyryl- CoA dehydratase	qPCR_hcd_f	GACTGATCCWAAAGGDGAYAGAAG	250	56	Alfreider et al.⁶
Thaumarchaea 1.1a	qPCR_hcd_r	CCYTTARCATCTGCWGGAATTGC	250	56	Alfreider et al.⁶
Ammonia oxidation pathway
Ammonia monooxygenase	GenAOAF	ATAGAGCCTCAAGTAGGAAAGTTCTA	100	55	Meinhardt et al.⁴⁰
Thaumarchaea	GenAOAR	CCAAGCGGCCATCCAGCTGTATGTCC	100	55	Meinhardt et al.⁴⁰

^aPrimer concentration (µmol); ^bTa: Annealing temperature (°C).