Table 1.

PCR amplification of genomic DNA from reference organisms

Species or isolateaSource or strainPCR products obtained with primer pairbHybridization with DSR probe
IIIIIIIV
SRs of the δ-Proteobacteria
Desulfovibrio vulgaris ATCC 29579+++++
 Desulfovibrio desulfuricans ATCC 27784+++2 ++
 Desulfovibrio africanus ATCC 19996(+)++
 Desulfovibrio sp. strain PT-2D. A. Stahl+++++
 Desulfovibrio oxyclinae Y. Cohen++++
 Desulfovibrio sp.D. Gevertz++++
 Desulfovibrio sp. strain G11M. J. McInerney+++++
 Desulfoarculum baarsii M. J. McInerney++
 Desulfobacterium niacini DSM 2650+++
 Desulfobacterium vacuolatum DSM 3385++ND
 Desulfococcus multivorans ATCC 33890+++
 Desulfonema ishimotoi Jade 02F. Widdel(+)+++
 Desulfonema ishimotoi Tokyo 01F. Widdel++(+)+
 Desulfonema limicola ATCC 33961++
 Desulfobotulus sapovorans ATCC 33892+++
 Desulfomonas pigra ATCC 29098+++++
 Desulfobacter latus ATCC 43918+++
 Desulfomicrobium baculatus DSM 1743+++
 Desulfobulbus propionicus ATCC 33891++
Nitrospira division SR
 Thermodesulfovibrio yellowstonii R. Devereux++
Thermodesulfobacterium division SR
 Thermodesulfobacterium commune ATCC 33708++
Gram-positive division SR
 Desulfotomaculum ruminis DLATCC 23193+++
δ-Proteobacteriawith “reverse” SR
 Beggiatoa sp. strain MS-81-1cD. Nelson
 Beggiatoa sp. strain OH-75-2aD. Nelson
 Beggiatoa sp. strain 81-6D. Nelson
 Chromatium vinosum ATCC 17899
 Thiobacillus denitrificans ATCC 25259
δ-Proteobacteria sulfite-respiring bacterium
 Shewanella putrefaciens ATCC 8071NDNDND
  • a SR, sulfate reducer.

  • b +, PCR product of the expected size; −, no PCR product; (+), low yield of PCR product; +2, two similar-sized PCR products; ND, not determined. PCR amplification of genomic DNA from 22 sulfate-reducing bacteria, 5 bacteria considered to possess a reverse-type sulfite reductase, and 1 bacterium having the capacity to respire sulfite with the DSR primers. The primer pair DSR1F-DSR4R (III) amplified the expected ∼1.9-kb fragment for all sulfate reducers tested. Primer pairs DSR1F-DSR3R (I), DSR2F-DSR4R (II), and DSR2F-DSR3R (IV) generated the expected ∼1.1-kb, ∼1.4-kb, and ∼0.5-kb fragments for only some of the sulfate-reducing bacteria analyzed. Sufficient quality of each genomic DNA for successful PCR amplification was demonstrated using conserved 16S rDNA-targeted primers (data not shown). Amplification products of all sulfate reducers with primer pair III hybridized specifically with a DNA probe complementary to a conserved region of the α subunit of the DSR.