TABLE 2.

PCR amplification of apsA gene fragments using genomic DNA of sulfate-reducing reference strains and selected characteristics

SpeciesaStrainbOxida-tioncToptd (°C)Genomic G+C content (mol %)PCR product obtained with primer paire:GenBank accession no.
APS-FW, APS-RVf (∼390 bp)APS7-F, APS8-R (∼900 bp)APS7a-F, APS8-R (∼900 bp)APS7b-F, APS8-R (∼900 bp)apsA16S rRNAdsrAB
Archaea, Euryarchaeota
    Archaeoglobus fulgidusDSM4304TC8346+g+gAE000988X05567, Y00275M95624
    Archaeoglobus profundusDSM5631TC8241++ (50)AF418134AF297529AF071499
    Archaeoglobus veneficusDSM11195TC75–8045.4++ (50)AF418132AF418181
Bacteria
    Nitrospira phylum
        Thermodesulfovibrio islandicusDSM12570TI6538+ (48)AF418113X96726AF334599
        Thermodesulfovibrio yellowstoniiDSM11347TI6529.5− (45)− (45)− (45)
    Thermodesulfobacteria phylum
        Thermodesulfobacterium communeDSM2178TI7034+ (48)AF418114AF418169AF334596
        Thermodesulfobacterium thermophilumDSM1276TI6531+ (48)AF418112AF334601
        Thermodesulfobacterium hveragerdenseDSM12571TI70–7440+ (48)AF418119X96725
    Firmicutes, “Clostridia,” Peptococcaceae
        Desulfotomaculum kuznetsoviiDSM6115TC60–6549+− (45)+ (59)+ (59)AF418152Y11569AF273031
        Desulfotomaculum thermobenzoicumDSM6193TC6253+− (45)+ (59)+ (59)AF418161L15628AF273030
        Desulfotomaculum geothermicumDSM3669TC5450++ (48)AF418115X80789AF273029
        Desulfotomaculum sapomandensDSM3223TC3848+ (45)− (59)AF418150AF168365
        Desulfotomaculum alkaliphilumDSM12257TC50–5541+ (48)− (59)AF418154AF097024AF418195
        Desulfotomaculum acetoxidansDSM771TC3738+ (48)− (59)− (59)AF418153Y11566AF271768
        Desulfotomaculum puteiDSM12395TI50–6547+− (45)+ (59)+ (59)AF418147AF053929AF273032
        Desulfotomaculum nigrificansDSM574TI5545+ (45)− (59)AF418154U33455
        Desulfotomaculum ruminisDSM2154TI2849− (45)l (45)l (45)AF418164Y11572
        Desulfotomaculum aeronauticumDSM10349TI3744+ (45)+ (45)+ (45)AF418156X98407AF273033
        Desulfotomaculum halophilumDSM11559TI3556.3+− (45)− (45)− (45)AF418167
        Desulfosporosinus orientisDSM8344I3045− (45)− (45)− (45)
    Proteobacteria delta subdivision
        “Desulfobacteraceaea
            Desulfobacter curvatusDSM3379TC28–3246+AF418107AF418175AF418199
            Desulfobacter postgateiDSM2034TC28–3346+ (45)l (45)+ (45)AF418157AF418180AF418198
            Desulfospira joergenseniiDSM10085TC26–3049.9l+AF418116X99637
            Desulfotignum balticumDSM7044C3062.4+AF418127AF418176
            Desulfobacula toluolicaDSM7467TC2842l+AF418128X70953
            Desulfobacterium autotrophicumDSM3382TC20–2648+AF418108AF418177AF418182
            “Desulfobacterium vacuolatum”DSM3385TC25–3045+AF418124AF418178AF418203
            Desulfocella halophilaDSM11763TI3435+AF418117AF022936AF418200
            Desulfonema ishimotoniiDSM9680TC3055++ (50)AF418135U45992
            Desulfonema magnumDSM2077TC3241.6+AF418122U45989
            Desulfofrigus oceanenseDSM12341TC1052.8l− (45)+ (55)AF418145AF099064
            Desulfofaba gelidaDSM12344TI752.5++AF418118AF099063AF334593
            Desulfococcus biacutusDSM5651TC28–3056.5ll (50)AF418151AJ277887
            Desulfococcus multivoransDSM2059TC3557.4++ (50)AF418136AF418173U58126/7
            Desulfosarcina variabilisDSM2060TC3351+AF418121M34407AF191907
            Desulfobacterium indolicumDSM3383TC2847++AF418123AJ237607
            “Desulfobacterium oleovorans”DSM6200TCn.a.in.a.++AF418126Y17698AF418201
            Desulfotalea psychrophilaDSM12343TI1046.8− (45)− (45)− (45)
        “Desulfobulbaceaea
            Desulfobulbus rhabdoformisDSM8777TI3150.6++AF418110U12253AJ250473
            Desulfobulbus elongatusDSM2908TI3559++l (55)AF418146X95180AF418202
            Desulfocapsa sulfexigensDSM10523TA3047.2++AF418131Y13672
            Desulfocapsa thiozymogenesDSM7269TI3050.7++ (45)+ (45)+ (45)AF418166
            Desulfofustis glycolicusDSM9705TI2856l+AF418130X99707AF418191
            Desulforhopalus sp. strain LsV 20DSM13038n.a.<20n.a.l (45)− (45)AF418160AF099057
            Desulforhopalus singaporensisDSM12130TI3150.6+ (45)− (45)+ (45)AF418163AF118453AF418196
        “Desulfovibrionalesa
            Desulfovibrio desulfuricans subsp. desulfuricans Essex 6DSM642TI3059++AF226708AF192153AJ249777
            Desulfovibrio intestinalisDSM11275TI3754.5–55.5++AF418106Y12254AF418183
            Desulfomonas pigraDSM749TI3766++AF418129AF192152AF418184
            Desulfovibrio termitidisDSM5308TI3567–68+++ (55)AF418142X87409AF418184
            Desulfovibrio vulgarisDSM644TI30–3665+g+gZ69372M34399U16723
            Desulfovibrio burkinensisDSM6830TI3767+++ (55)AF418143AF053752AF418186
            Desulfovibrio fructosovoransDSM3604TI3564l+AF418109AF050101AF418187
            Desulfovibrio africanusDSM2603TI30–3665++ (50)+ (55)AF418140X99236AF271772
            Desulfovibrio giganteusDSM4370TI3756++ (50)+ (55)AF418141AF418170
            Desulfovibrio profundusDSM11384TI2553++ (50)AF418133AF418172
            Desulfomicrobium baculatumDSM1743TI28–3757++AF418120
            Desulfomicrobium apsheronumDSM5918TI25–3052++AF420281U64865AF418188
            Desulfohalobium retbaenseDSM5692TI37–4057.1l+ (50)AF418125X99235AF418190
            Desulfonatronum lacustreDSM10312TI37–4057.3++ (50)AF418137AF418171AF418189
            Desulfonatronovibrio hydrogenovoransDSM9292Tn.a.3748.6++AF418111X99234AF418197
        “Syntrophobacteraceaea
            Syntrophobacter woliniiDSM2805MTIn.d.jn.d.++ (45)+ (45)+ (45)AF418165X70905AF418192
            Syntrophobacter pfennigiiDSM10092TI3757.3++ (45)+ (45)+ (45)AF418168X82875
            Syntrophobacter fumaroxidansDSM10017TI3760.6++ (45)+ (59)+ (59)AF418138X82874AF418193
            Desulforhabdus amnigenaDSM10338TC3752.5++ (45)+ (59)+ (59)AF418139X83274AF337901
            Thermodesulforhabdus norvegicaDSM9990TC6051++ (45)+ (45)+ (59)AF418159U25627AF334597
            Desulfacinum infernumDSM9756Tn.a.6064++ (45)+ (59)+ (59)AF418144L27426AF418194
            Desulfacinum hydrothermaleDSM13146TC6059.5++ (45)+ (50)AF418148AF170417
        “Nitrospinaceaea
            Desulfomonile tiedjeiDSM6799TC3749++ (45)+ (45)+ (50)AF418162M26635AF334595
            “Desulfarculus baarsii”DSM2075TC3766++ (45)+ (45)+ (55)AF418149AF418174AF334600
            “Desulfobacterium anilini”DSM4660TC3559.1+ (45)+ (45)+ (45)AF418158AJ237601
            Desulfobacca acetoxidansDSM11109TC3751.5− (48)− (45)− (45)
  • a Phylum and family names according to the taxonomic outline of Bergey’s Manual of Systematic Bacteriology (http://www.cme.msu.edu/Bergeys/april2001-genus.pdf).

  • b DSMZ strain numbers. T, type strain.

  • c C, complete oxidation of organic carbon substrates; I, incomplete oxidation; A, chemolithoautotrophic growth.

  • d Topt, optimum growth temperature.

  • e PCR annealing temperatures in degrees Celsius are in parentheses. Boldface, no PCR product obtained. l, low yield.

  • f PCR annealing temperature 60°C according to Deplancke et al. (7).

  • g Binding of the primer pair deduced from sequence.

  • h Sequences from this study are in boldface.

  • i n.a., not available.

  • j n.d., not determined.