TABLE 1.

Distribution of OTUs in the oyster reef 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)993.97211.5
    Group P (ORB 19)Beta proteobacterium A1020 (AF236013)933.17145.0
    Group S (ORB 14)Uncultured proteobacterium clone Bol37 (AY193142)971.5996.6
    Group U (ORB 154)Gamma proteobacterium PII_GH4.2.G5 (AY162068)991.59211.8
    ORB 4Uncultured bacterium Br-z23 (AF506993)990.79ND
    ORB 17Unidentified gamma proteobacterium (AB015254)920.79ND
    ORB 21Dechloromarinus chlorophilus (AF170359)950.79ND
    ORB 36Unidentified gamma proteobacterium (AB015254)920.79ND
    ORB 52Uncultured gamma proteobacterium Sva0091 (AJ240987)960.79ND
    ORB 101Uncultured bacterium clone Hw124 (AF497583)920.79ND
    ORB 107Pseudoalteromonas sp. AS-43 (AJ391204)990.79ND
    ORB 112Uncultured gamma proteobacterium partial (AJ535246)950.79ND
    ORB 125Uncultured gamma proteobacterium Sva0091 (AJ240987)950.79ND
    ORB 129Thalassomonas viridans (AJ294747)950.79ND
    ORB 146Uncultured proteobacterium clone Bol37 (AY193142)980.79ND
    ORB 158Gamma proteobacterium MBIC3957 (AB021682)860.79ND
    ORB 163Uncultured beta proteobacterium partial (AJ422174)890.79ND
    ORB 172Marine gamma proteobacterium MKT112 gene (AB076562)860.79ND
    ORB 182H. obtusa (X58198)880.79ND
    Total for group22.17
δ-Proteobacteria
    Group Fc (ORB 23)Desulfobacterium catecholicum (AJ237602)952.3891.2
    Group Zc (ORB 143)Uncultured delta proteobacterium Sva1041 (AJ240984)940.7990.8
    Group AAc (SBB 68)Olavius algarvensis sulfate-reducing endosymbiont (AF328857)940.7992.0
    ORB 29Uncultured delta proteobacterium partial (AJ535245)960.79ND
    ORB 42Uncultured delta proteobacterium Sva1041 (AJ240984)930.79ND
    ORB 64Unidentified eubacterium (AJ007373)920.79ND
    ORB 92Uncultured delta proteobacterium Sva0485 (AJ241001)950.79ND
    ORB 118Olavius algarvensis sulfate-reducing endosymbiont (AF328857)930.79ND
    ORB 127Geobacter sp. Ala-6 (AF019929)870.79ND
    ORB 137Uncultured delta proteobacterium Sva1033 (AJ240983)950.79ND
    ORB 138Bdellovibrio sp. JS10 (AF084863)910.79ND
    ORB 149Uncultured delta proteobacterium Sva0566 (AJ241000)980.79ND
    ORB 153Delta proteobacterium S2552 (AF468969)890.79ND
    ORB 162Uncultured delta proteobacterium Sva0566 (AJ241000)940.79ND
    Total for group12.65
CFB group
    Group K (ORB 30)Uncultured CFB group bacterium FL13A07 (AF446287)912.3891.6
    Group X (ORB 34)CFB group bacterium RW262 (AF493694)932.38>1,000
    Group W (ORB 39)Uncultured bacterium clone s22 (AY171331)961.5993.0
    Group V (ORB 43)CFB group bacterium RW262 (AF493694)901.5995.6
    Group L (ORB 141)Flavobacteriaceae strain SW084 (AF493687)931.5993.9
    Group Yc (ORB 119)Salt marsh clone LCP-72 (AF286039)970.7996.3
    Group Mc (ORB 120)Salt marsh clone LCP-72 (AF286039)960.7996.0
    ORB 3Uncultured CFB group bacterium (AJ441241)900.79ND
    ORB 8Uncultured Cytophagales (AF361205)920.79ND
    ORB 16Uncultured CFB group bacterium partial (AJ441238)930.79ND
    ORB 24Uncultured bacterium clone ARKIA-105 (AF468278)890.79ND
    ORB 26Uncult. CFB group bacterium clone SM2D04 (AF445721)910.79ND
    ORB 33CFB group bacterium RW262 (AF493694)900.79ND
    ORB 40Uncultured Cytophagaceae bacterium clone 1-13 (AY094494)900.79ND
    ORB 44Uncultured CFB group bacterium clone SM2D04 (AF445721)910.79ND
    ORB 61Flavobacteriaceae bacterium BIA (AY177722)920.79ND
    ORB 102Uncultured bacterium clone CARB_ESS_9 (AY239540)900.79ND
    ORB 140Uncultured Cytophagales bacterium clone CD4G5 (AY038505)900.79ND
    ORB 145Bacteroidetes bacterium GMD13F04 (AY162116)890.79ND
    ORB 148Unidentified Cytophagales partial (AJ007871)880.79ND
    ORB 187Flavobacteriaceae strain SW084 (AF493687)930.79ND
    Total for group22.17
Planctomyces phylum
    Group Bc (ORB 9)Uncultured planctomycete EC-149 (AF287048)971.59561.5
    Group Ac (SBB 58)Uncultured bacterium clone 33-FL67B99 (AF469406)951.59560.8
    Group Nc (ORB 6)Uncultured planctomycete EC-149 (AF287048)960.79>1,000
    Group Rc (ORB 97)Uncultured bacterium gene (AB100005)950.79842.6
    Group Ec (ORB 156)Uncultured bacterium clone 33-FL67B99 (AF469406)920.79560.5
    ORB 18Uncultured planctomycete partial (BX294700)920.79ND
    ORB 35Uncultured bacterium #0319-7F4 (AF234144)890.79ND
    ORB 41Uncultured Pirellula clone 6N14 (AF029078)950.79ND
    ORB 48Planctomyces maris (strain DSM 8797T) (AJ231184)910.79ND
    ORB 88Uncultured Crater Lake bacterium CL500-15 (AF316773)920.79ND
    ORB 103Uncultured planctomycete partial (BX294885)950.79ND
    ORB 170Uncultured planctomycete partial (BX294710)890.79ND
    ORB 180Uncultured planctomycete partial (BX294710)880.79ND
    ORB 186Uncultured soil bacterium clone S165 (AF507705)880.79ND
    Total for group12.66
Holophaga-Acidobacterium phylum
    Group O (ORB 2)Uncultured bacterium clone NMS8.79WL (AF432679)931.59355.9
    ORB 5Uncultured Holophaga-Acidobacterium Sva0725 (AJ241003)930.79ND
    ORB 31Sulfate-reducing bacteria gene for 16S rDNA (X80922)860.79ND
    ORB 81Holophaga sp. oral clone CA002 (AF385537)870.79ND
    ORB 100Uncultured Holophaga-Acidobacterium Sva0725 (AJ241003)960.79ND
    ORB 110Uncultured Holophaga sp. (AJ535239)950.79ND
    ORB 114Uncultured Holophaga-Acidobacterium Sva0515 (AJ241004)920.79ND
    ORB 132Hydrothermal vent eubacterium PVB_OTU_9A (U15118)950.79ND
    ORB 160Uncultured Holophaga-Acidobacterium Sva0725 (AJ241003)890.79ND
    ORB 166Uncultured delta proteobacterium clone WCB41 (AY217485)930.79ND
    ORB 188Uncultured Holophaga-Acidobacterium Sva0515 (AJ241004)890.79ND
    Total for group9.49
Verrucomicrobia
    Group Cc (ORB 15)Unidentified eubacterium LD29 (AF009975)961.59218.6
    ORB 66Unidentified eubacterium LD29 (AF009975)950.79ND
    Total for group2.38
Others
    Group J (ORB 77)Odontella sinensis complete chloroplast genome (Z67753)963.97843.1
    Group Ic (ORB 123)Uncultured marine eubacterium HstpL35 (AF159636)972.38>1,000
    Group Q (ORB 57)Uncultured delta proteobacterium CtaxPhil-2 (AF259630)961.5925.7
    Group Hc (SBB 138)Bacterial sp. (X89322)970.7980.9
    ORB 1Uncultured myxobacterium Sva1009 (AJ297456)950.79ND
    ORB 10Salt marsh clone LCP-68 16S (AF286033)960.79ND
    ORB 46Uncultured soil bacterium PBS-II-37 partial (AJ390447)900.79ND
    ORB 63Uncultured proteobacterium clone ccs202 (AY133065)900.79ND
    ORB 65Bacterial sp. gene for 16S rRNA (isolate 4911) (X89322)930.79ND
    ORB 98Uncultured high-G + C gram-positive bacterium Sva0389 (AJ240976)930.79ND
    ORB 111Uncultured marine eubacterium HstpL35 (AF159636)970.79ND
    ORB 115Uncultured bacterium clone Bol11 (AY193132)920.79ND
    ORB 121Uncult. candidate division WS3 bacterium clone LD1-PA13 (AY114311)910.79ND
    ORB 157Bacterial sp. gene for 16S rRNA (isolate 4911) (X89322)970.79ND
    ORB 165Uncultured marine eubacterium HstpL35 (AF159636)980.79ND
    ORB 178Uncultured Acidobacterium-Holophaga (AF423363)960.79ND
    Total for group19.00
  • a OTUs were named with the prefix ORB for the oyster reef biofilm and SBB 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.