TABLE S2. Primers used in this study.

Loci / N16961
chromosome / Primer set name / Primer sequence (5’-3’) / Reference
16S rDNA
(Vibrio cholerae specific) / 1 / VC490
VC1261R / AATACCTTAATCATTTGACGTTACCT
GCTCCACCTCGCGGTATC / (4)
and this study
16S rDNA
(eubacterial) / 1 /

27F

1492R / AGAGTTTGATCCTGGCTCAG
GGTTACCTTGTTACGACTT / (2)
23S rDNA / 1 / BLF 188-20
BLR 1686-20 / GGAACTGAAACATCTAAGTA
GGGGCCATTTTGCCGAGTTC / (6)
Vibrio cholerae-Vibrio mimicus specific
Interspacer Region
Types 1 and 2 / 1 / pr16S-1541F
pr23S-25R / YGGNTGGATCACCTCCTT
TGACTGCCMRGGCATCCA / (1) and this study
Deoxyribodipyrimidine photolyase (phrB-1) / 1 / PHRB-1F
PHRB-1R / GATTTACGAGTGAACGATAACCCG
ATGCCGTCTAACCCATTGCG / this study
Deoxyribodipyrimidine photolyase (phrB-2) / 2 / PHRB-2F
PHRB-2R / CCGATTTGATTTGGCGACG
AAGTAGGGTGAGAGCGAACTGGTG / this study
DNA Helicase II (uvrD) / 1 / UVRDF
UVRDR / CCAATAATAGCGAGCGGATGG
CCAGCAGACCAGAGGTTTTTACC / this study
DNA Helicase IV (helD) / 2 / HELDF
HELDR / AGAGGCGTGTTTTGGGGAAC
TGCTTGAGTTTGCTGTCATTCG / this study
Integrase/recombinase XerC (xerC) / 1 / XERCF
XERCR / GGGATGAAAGCCAGCAGTATCG
TTGTGCCTGTCCAGCAAACCAC / this study
Site-specific recombinase Intl4 (intl4) / 2 / INTL4F
INTL4R / CCCATCAAGTTACTCTACGGTTCG
AGTCACGGTCTTTTCAATCCCC / this study
Panhandle PCR
adaptor ligation / -- / Adaptor1
Adaptor2 / CTAATACGACTCACTATAGGGCTCG-AGCGGCCGCCCGGGCAGGT
Phos-ACCTGCCCGG-NH2 / (3, 5)
Panhandle PCR amplification and sequencing / -- / AP1
AP2 / GGATCCTAATACGACTCACTATAGGG
AATAGGGCTCGAGCGGC / (3, 5)

References for Table S2.

1. Chun, J., A. Huq, and R. R. Colwell. 1999. Analysis of 16S-23S intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. App. Environ. Microbiol. 65:2202-2208.

2. Delong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U. S. A. 89:5685-5689.

3. Egan, S., S. James, C. Holmstrom, and S. Kjelleberg. 2002. Correlation between pigmentation and antifouling compounds produced by Pseudoalteromonas tunicata. Environ. Microbiol. 4:433-442.

4. Nishimura, M., K. Kita-Tsukamoto, K. Kogure, K. Ohwada, and U. Simidu. 1993. A new method to detect viable bacteria in natural seawater using 16S rRNA oligonucleotide probe. J. Oceanography 49:51-56.

5. Siebert, P. D., A. Chenchik, D. E. Kellogg, K. A. Lukyanov, and S. A. Lukyanov. 1995. An improved PCR method for walking in uncloned genomic DNA. Nuc. Acids. Res. 23:1087-1088.

6. Van Camp, G., S. Chapelle, and R. De Wachter. 1993. Amplification and sequencing of variable regions in bacterial 23S ribosomal RNA genes with conserved primer sequences. Curr. Microbiol. 27:147-151.