TABLE 2.

Distribution of OTUs in the sand bottom biofilm 16S rDNA clone library and phylogenetic relationships

Group and OTUa16S rDNA identification of closest neighbor (accession no.)Sequence similarity (%)Abundanceb in community (%)Length of 5′ T-RFd (HhaI, in bp)
γ-Proteobacteria
    Group Dc (ORB 49)Uncultured bacterium Br-z23 (AF506993)999.63211.5
    SBB 7Pseudoalteromonas sp. AS-43 (AJ391204)990.74ND
    SBB 43Pseudoalteromonas sp. AS-43 (AJ391204)990.74ND
    Total for group11.11
δ-Proteobacteria
    Group Fc (ORB 23)Desulfobacterium catecholicum (AJ237602)951.4891.2
    Group Zc (ORB 143)Uncultured delta proteobacterium Sva1041 (AJ240984)940.7490.8
    Group AAc (SBB 68)Olavius algarvensis sulfate-reducing endosymbiont (AF328857)940.7492.0
    SBB 18Uncultured Desulfuromonadales bacterium (AY177804)890.74ND
    Total for group3.7
CFB group
    Group Mc (ORB 120)Salt marsh clone LCP-72 (AF286039)960.7496.0
    Group Yc (ORB 119)Salt marsh clone LCP-72 (AF286039)970.7496.3
    SBB 9Uncultured bacterium partial clone Hyd89-65 (AJ535255)960.74ND
    SBB 40Flexibacter aggregans subsp. catalaticus gene (AB078042)940.74ND
    SBB 153CFB group bacterium RW262 (AF493694)880.74ND
    Total for group3.7
Planctomyces phylum
    Group Bc (ORB 9)Uncultured planctomycete EC-149 (AF287048)9715.56561.5
    Group Ac (SBB 58)Uncultured bacterium clone 33-FL67B99 (AF469406)9614.81560.8
    Group Ec (ORB 156)Uncultured bacterium clone 33-FL67B99 (AF469406)927.41560.5
    Group Nc (ORB 6)Uncultured planctomycete EC-149 (AF287048)960.74>1,000
    Group Rc (ORB 97)Uncultured bacterium gene (AB100005)950.74842.6
    SBB 12Uncultured planctomycete clone CY0ARA031G01 (BX294851)900.74ND
    SBB 15Uncultured Pirellula clone 6N14 (AF029078)950.74ND
    SBB 33Marine eubacterial sp. (aggregate agg8) PCR generated (L10942)940.74ND
    SBB 73Uncultured Pirellula clone 6N14 (AF029078)930.74ND
    SBB 76Uncultured bacterium clone SG2-79 (AY135912)930.74ND
    SBB 85Uncultured Planctomyces clone 7F15 (AF029079)980.74ND
    SBB 107Uncultured planctomycete EC-149 (AF287048)970.74ND
    SBB 139Uncultured bacterium clone 33-FL67B99 (AF469406)970.74ND
    SBB 141Planctomyces sp. partial (X81956)910.74ND
    Total for group45.92
Holophaga-Acidobacterium
    SBB 45Uncultured Holophaga-Acidobacterium Sva0725 (AJ241003)960.74ND
    SBB 71Uncultured Holophaga-Acidobacterium Sva0725 (AJ241003)930.74ND
    Total for group1.48
Verrucomicrobia
    Group Cc (ORB 15)Unidentified eubacterium LD29 (AF009975)9613.33218.6
    SBB 97Unidentified eubacterium LD29 (AF009975)930.74ND
    SBB 103Unidentified eubacterium LD29 (AF009975)950.74ND
    SBB 146Uncultured Verrucomicrobia Arctic 95D-9 (AY028220)920.74ND
    Total for group15.55
Syntrophus
    SBB 27Unidentified bacterium partial (AJ518378)910.74ND
    SBB 128Unidentified bacterium partial, clone Neu4P1-54 (AJ518378)910.74ND
    SBB 135Unidentified bacterium partial, clone Neu4P1-54 (AJ518378)900.74ND
    Total for group2.22
Gram-positive branch
    SBB 16Uncultured high-G + C gram-positive bacterium Sva1007 (AJ241019)920.74ND
    SBB 30Uncultured hydrocarbon seep bacterium BPC063 (AF154093)960.74ND
    SBB 152Uncultured high-G + C gram-positive bacterium Sva0389 (AJ240976)960.74ND
    Total for group2.22
Others
    Group G (SBB 94)Bacterial sp. (X89322)<300 bp3.7212.6
    Group Hc (SBB 138)Bacterial sp. (X89322)<200 bp2.2280.9
    Group T (SBB 144)Bacterial sp. (X89322)<200 bp1.4881.0
    Group Ic (ORB 123)Uncultured marine eubacterium HstpL35 (AF159636)970.74>1,000
    SBB 3Uncultured bacterium clone BT60DS4BD12 (AF365742)980.74ND
    SBB 46Uncultured bacterium partial, clone JG34-KF-153 (AJ532721)910.74ND
    SBB 50Bacterial sp. gene (isolate 4911) (X89322)960.74ND
    SBB 67Bacterial sp. gene (X89322)960.74ND
    SBB 86Uncultured bacterium partial (AJ306763)900.74ND
    SBB 119Bacterial sp. gene (X89322)930.74ND
    SBB 121Uncultured epsilon proteobacterium clone 33-FL58B00 (AF468777)930.74ND
    SBB 145Uncultured bacterium gene clone Rs-H34 (AB089123)910.74ND
    Total for group14.06
  • a OTUs were named with the prefix 5 for the oyster reef habitat and the prefix 6 for the muddy sand bottom habitat. Groups comprise more than one member.

  • b Relative abundance was calculated as follows: relative abundance = (n/N) × 100, where n is the number of clones representing the same OTU and N is the total number of clones in the library. The added relative abundances for each phylogenetic group are shown in bold.

  • c OTU shared between biofilms from the oyster reef habitat and the muddy sand bottom habitat.

  • d Lengths of 5′ T-RFs were experimentally determined.