TABLE 2.
Primers used for phnJ sequencing and RT-PCR analysisa
| Target (strain[s]) | Application | Forward primer (sequence) | Reverse primer (sequence) | Source or references |
|---|---|---|---|---|
| phnJ | PCR | PhnJoc1 (AARGTRATMGAYCARGG) | PhnJoc2 (CATYTTYGGATTRTCRAA) | 46, 47 |
| phnJ1 (LM-1, LM-5, and LM6-1) | RT-PCR | phnJ-F1 (ACCATCATCCAGACGCGGCA) | phnJ-R1 (AGCTTGACGTGCATCAGGCC) | This study |
| phnJ2 (LM-Y) | RT-PCR | phnJ-F2 (TCAGACGCGTCACCGTATT) | phnJ-R2 (CTTCGTACAGTTTGACCTGC) | This study |
a
Degenerate primers were used to amplify and sequence phnJ from all isolates; specific primers were designed based on the sequences to use for qPCR. Strains LM-1, LM-5, and LM6-1 are members of Alphaproteobacteria that are closely related to each other, and the same primer pair was used for all three. Primers for LM-Y were slightly different but were complementary to the same region of the gene and generated a product of the same size.