TABLE 2.

Primer sets for PCR and qPCR.

Name	Target	Length	Primers	qPCR efficiency
phoD	Gammaproteobacteria	795 bp	F: 5′-TWCAYCTYGGTGAYTACATTTATGARTA-3′ R: 5′-TCRACRKRGTARCCATCCCAWGCRTC-3′
phoX*	Gammaproteobacteria	586 bp	F: 5′-GGGNACTTAYYTMACBTGYGAA-3′ R: 5′-GDCKATCCATBGKBGTTGC-3′
phoD1	Alteromonas spp.	98 bp	F: 5′-TATAYATGCTCGACACCCGC-3′ R: 5′-AAAGCGYGCTTGGTCAAACG-3′	95%
phoD2	Vibrio spp.	103 bp	F: 5′-CGGTTTAGTTGCYCAGTCGC-3′ R: 5′-ATTCCAAGTTGCGTCGTGCG-3′	82%
phoX1	Vibrio splendidus**	91 bp	F: 5′-GAAGCGAAATGGGACCCACG-3′ R: 5′-TCGCCACATATAGMGTGCCT-3′	104%
phoX2	Vibrio alginolyticus	189 bp	F: 5′-GCTTGGCGATGGGTGACAAG-3′ R: 5′-CAACTAAATCCGCCGCACCC-3′	101%

The reverse primers of the Gammaproteobacterial phoD and phoX primers were used for cDNA synthesis. *From Sebastian and Ammerman (2009). All other primers were designed for this study. **Primer set phoX1 is expected to amplify other Vibrio spp. including V. crassostreae and V. chagasii; however, most of the phoX1 clones and metatranscriptome reads had high identity to V. splendidus.