TABLE 1.
Summary of DGGE band sequencing analysis
| Sample and band no. | Enrichment conditions | Genus affiliation (RDP II classifier)a | Best database match (GenBank accession no.)b | Identity (%)c | Characteristic/origin of closest database hitd | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Emiliania huxleyi cultures | ||||||||||
| 1 | Strain 1516, methanol preenrichment, 50 μM DMS | Methylophaga (Gammaproteobacteria) | Methylophaga thalassica (X95460) | 537/548 (97) | Marine methylotrophic bacterium | |||||
| 4 | Strain 1516, 50 μM DMS, then subcultured with 500 μM DMS | Unclassified Rhodobacteraceae | Uncultured bacterium clone E4aB11 (DQ103616) | 553/559 (98) | Hypersaline endoevaporitic microbial mat | |||||
| 2 | Pooled strains, increasing DMS concn | Unclassified Flavobacteriaceae | Uncultured Flavobacteria bacterium clone V1_026 (AY907285) | 495/499 (99) | Culture of Thalassiosira rotula 04 | |||||
| 3 | Pooled strains, increasing DMS concn | Alcanivorax (Gammaproteobacteria) | Fundibacter jadensis (AJ001150) | 581/586 (99) | Intertidal North Sea sediment; hydrocarbon degrader | |||||
| 6, clone 1 | Pooled strains, methanol preenrichment, 50 μM DMS | Methylophaga (Gammaproteobacteria) | Methylophaga thalassica (X95460) | 573/586 (97) | Marine methylotrophic bacterium | |||||
| 6, clone 2 | Pooled strains, methanol preenrichment, 50 μM DMS | Unclassified Gammaproteobacteria | Uncultivated gammaproteobacterium clone YC499B15_AB (AY701432) | 448/482 (92) | Culture of Gymnodinium catenatum YC499B15 | |||||
| Pooled methyl halide enrichments | ||||||||||
| 10 | 50 μM DMS | Unclassified Betaproteobacteria | Uncultured betaproteobacterium clone 139_16sGbFL1 (AY786220) | 521/534 (97) | Guaymas Basin background deep water | |||||
| 7 | 50 μM DMS, then subcultured with 500 μM DMS | Unclassified bacteria | Uncultured proteobacterium clone IAFDn69 (AY090126) | 289/290 (99) | Marine methanol-fed denitrification bioreactor | |||||
| 11 | 50 μM DMS, then subcultured with 500 μM DMS | Alcanivorax (Gammaproteobacteria) | Alcanivorax sp. strain DG813 (AY258105) | 518/535 (96) | Culture of Gymnodinium catenatum | |||||
| 12 | 50 μM DMS, then subcultured with 500 μM DMS | Unclassified Myxococcales | Uncultured bacterium clone BG.c4 (DQ228369) | 533/570 (93) | Bench Glacier | |||||
| 13 | 50 μM DMS, then subcultured with 500 μM DMS | Unclassified Sphingomonadaceae | Uncultured forest soil bacterium clone DUNssu153 (AY913360) | 490/506 (96) | 0-20-cm bulk soil, Duennwald forest | |||||
| 8 | Methanol preenrichment, then 50 μM DMS | Unclassified bacteria | Unidentified bacterium clone 1959 (AF097803) | 539/549 (98) | Activated sludge | |||||
| 9 | Methanol preenrichment, then 50 μM DMS | Sphingopyxis | Sphingomonas sp. strain SA-3 (AF327069) | 524/526 (99) | ||||||
| 14 | Methanol preenrichment, then 50 μM DMS | Unclassified Alphaproteobacteria | Alphaproteobacterium strain AP-25 (AY145562) | 451/474 (95) | Dilution culture (10−6) from marine section of Weser estuary | |||||
| Achmelvich Bay | ||||||||||
| 16 | 50 μM DMS | Alcanivorax (Gammaproteobacteria) | Alcanivorax sp. strain DG813 (AY258105) | 533/533 (100) | Culture of Gymnodinium catenatum | |||||
| 15 | 50 μM DMS, then subcultured with 500 μM DMS | Methylophaga (Gammaproteobacteria) | Methylophaga thalassica (X95460) | 518/529 (97) | Marine methylotrophic bacterium | |||||
| 25 | Methanol preenrichment, then 50 μM DMS | Alcanivorax (Gammaproteobacteria) | Alcanivorax sp. strain DG813 (AY258105) | 584/586 (99) | Culture of Gymnodinium catenatum | |||||
| 26 | Methanol preenrichment, then 50 μM DMS | Unclassified Alphaproteobacteria | Marine bacterium SCRIPPS_94 (AF359545) | 557/557 (100) | Culture of Scrippsiella trochoidea NEPCC 15 | |||||
| Coral Beach, rock pool | ||||||||||
| 17 | 50 μM DMS, then subcultured with 500 μM DMS | Methylophaga (Gammaproteobacteria) | Methylophaga thalassica (X95460) | 571/584 (97) | Marine methylotrophic bacterium | |||||
| 18 | Formate preenrichment, then 50 μM DMS | Methylophaga (Gammaproteobacteria) | Methylophaga thalassica (X95460) | 506/534 (94) | Marine methylotrophic bacterium | |||||
| 20 | 50 μM DMS, then subcultured with 500 μM DMS | Alcanivorax (Gammaproteobacteria) | Alcanivorax sp. strain DG813 (AY258105) | 532/532 (100) | Culture of Gymnodinium catenatum | |||||
| 21 | 50 μM DMS | Unclassified Alphaproteobacteria | Marine bacterium SCRIPPS_94 (AF359545) | 510/510 (100) | Culture of Scrippsiella trochoidea NEPCC 15 | |||||
| 22 | 50 μM DMS | Unclassified bacteria | Uncultured Actinomycetales bacterium (DQ228712) | 414/445 (93) | Cave rock | |||||
| English Channel | ||||||||||
| 29 | Nov 2004, formate preenrichment, 50 μM DMS | Sphingobacteria (Bacteroidetes) | Uncultured bacterium clone 72-ORF19 (DQ376575) | 407/423 (96) | Aerobic sequencing batch reactor | |||||
| 30 | Nov 2004, formate preenrichment, 50 μM DMS | Methylophaga (Gammaproteobacteria) | Uncultured Methylophaga sp. clone JL-ECS-X17 (AY663963) | 525/536 (97) | East China Sea | |||||
| 31 | Nov 2004, formate preenrichment, 50 μM DMS | Gammaproteobacteria | Uncultured bacterium clone WIM-Mm-3 (AY309182) | 352/385 (91) | Peat | |||||
| 32 | Nov 2004, formate preenrichment, 50 μM DMS | Alcanivorax (Gammaproteobacteria) | Alcanivorax sp. strain DG813 (AY258105) | 513/535 (95)e | Culture of Gymnodinium catenatum | |||||
| 33 | Nov 2004, formate preenrichment, 50 μM DMS | Rhodobacteraceae (Alphaproteobacteria) | Uncultured bacterium clone ELB16-059 (DQ015815) | 500/504 (99) | Lake Bonney (Antarctica) | |||||
| 34 | Nov 2004, formate preenrichment, 50 μM DMS | Clostridia (Firmicutes) | Uncultured bacterium clone s101 (AY171344) | 482/495 (97) | Marine sediment | |||||
| 35 | Nov 2004, acrylate preenrichment, 50 μM DMS | Alcanivorax (Gammaproteobacteria) | Alcanivorax sp. strain DG813 (AY258105) | 484/484 (100) | Culture of Gymnodinium catenatum | |||||
| 37 | Nov 2004, 50 μM DMS | Bacteroidetes | Uncultured alphaproteobacterium clone 131637 (AY922203) | 527/528 (99) | Gray whale bone, Pacific Ocean | |||||
| 38 | Nov 2004, 50 μM DMS | Gammaproteobacteria | Uncultured bacterium clone WIM-Mm-3 (AY309182) | 352/385 (91) | Peat | |||||
| 40 | Nov 2004, 50 μM DMS | Clostridiales (Firmicutes) | Uncultured bacterium clone s101 (AY171344) | 503/513 (98) | Marine sediment | |||||
| 42 | Nov 2004, 50 μM DMS | Alphaproteobacteria | Uncultured alphaproteobacterium clone P_wp0211 (AY186195) | 501/502 (99) | Deep-sea sediment | |||||
| 43 | May 2005, 50 μM DMS | Alphaproteobacteria | Kordiimonas gwangyangensis strain GW14-5 (AY682384) | 417/450 (92) | Degrader of polycyclic aromatic hydrocarbons | |||||
| 47 | May 2005, 50 μM DMS, 4 mM bicarbonate, 2.5 mM thiosulfate | Erythrobacter (Alphaproteobacteria) | Uncultured Erythrobacter sp. clone JL-ETNP-Y43 (AY726907) | 457/458 (99) | 1,000-m depth of tropical eastern North Pacific | |||||
| 48 | May 2005, 50 μM DMS, 4 mM bicarbonate | Rhodobacteraceae (Alphaproteobacteria) | Uncultured bacterium clone ELB16-059 (DQ015815) | 505/510 (99) | Lake Bonney (Antarctica) | |||||
| 49 | May 2005, 50 μM DMS, 4 mM bicarbonate, 2.5 mM thiosulfate | Gelidibacter (Bacteroidetes) | Uncultured CFB group bacterium clone DBS2 (AF466705) | 513/515 (99) | Sludge sample of a digestion basin of a mariculture system | |||||
| 50 | May 2005, 50 μM DMS, 4 mM bicarbonate, 2.5 mM thiosulfate | Piscirickettsiaceae (Gammaproteobacteria) | Uncultured gammaproteobacterium clone HMMVCen-15 (AJ704664) | 474/483 (98) | Marine sediment of Haakon Mosby mud volcano | |||||
a
Using the program “classifier” at the Ribosomal Database Project II (RDP II) website (http://rdp.cme.msu.edu/classifier/classifier.jsp) and the default confidence threshold of 80%.
b
Using BLASTn against NR database at NCBI.
c
Identities according to BLASTn output; gaps were ignored.
d
Source data based on GenBank entry.
e
Poor sequence quality.