Table 1.
Sample overview, amplification results and sequencing statistics for masD/assA gene clone libraries from pristine and seepage-impacted environmental samples and enrichment cultures.
| Sample | Sample type, location, coring methoda | Sediment depth (cm) | Amplification resultb | Number of clonesc | Number of OTUsd | Good’s coveraged |
|---|---|---|---|---|---|---|
| Pristine sediments | ||||||
| M1 | Marine sediment, Aarhus Bay, RC | 0–50 | ++ (45) | 68 | 22 | 0.88 |
| SKA1 | Marine sediment, Skagerrak, GC | 0–46 | ++ (55) | 70 | 17 | 0.92 |
| SKA4 | Marine sediment, Skagerrak, GC | 13–53 | ++ (55) | 59 | 15 | 0.86 |
| SKA51e | Marine sediment, Lille Belt, GC | 3–50 | ++ (45) | 80 | 22 | 0.9 |
| SKA52e | Marine sediment, Lille Belt, GC | 70–105 | ++ (45) | 57 | 18 | 0.84 |
| M5f | Marine sediment, Aarhus Bay, RC | 4–52 | n.a. | |||
| BBf | Fjord sediment, Limfjorden, RC | 0–40 | n.a. | |||
| Seepage-impacted sediments | ||||||
| LF1f,g | Eutrophic fjord sediment, Limfjorden, RC | 0–60 | n.a. | |||
| LF2g | Eutrophic fjord sediment, Limfjorden, RC | 0–40 | ++ (45) | 51 | 17 | 0.9 |
| LF3g | Eutrophic fjord sediment, Limfjorden, RC | 0–50 | ++ (45) | 78 | 27 | 0.83 |
| LF4f,g | Eutrophic fjord sediment, Limfjorden, RC | 0–60 | n.a. | |||
| LF5g | Eutrophic fjord sediment, Limfjorden, RC | 0–50 | ++ (45) | 80 | 15 | 0.95 |
| LF6g | Eutrophic fjord sediment, Limfjorden, RC | 0–70 | ++ (45) | 79 | 18 | 0.96 |
| SKA3 | Marine sediment, Skagerrak, RC | 0–45 | ++ (45) | 69 | 13 | 0.96 |
| BS | Coastal sandy sediment, Bangsbostrand, PC | 0–10 | + (55) | 63 | 13 | 0.92 |
| MV | Marine sediment, Middle Valley (Juan de Fuca Ridge) | 0–30 | + (55) | 11 | 4 | 0.82 |
| Enrichments | ||||||
| MV25C3 | Propane-degrading enrichment, 25°C | – | ++ (55) | 16 | 1 | 1 |
| MV25C4 | Butane-degrading enrichment, 25°C | – | + (45) | 24 | 1 | 1 |
| MV55C3 | Propane-degrading enrichment, 55°C | – | – | – | – | – |
| MV55C4 | Butane-degrading enrichment, 55°C | – | – | – | – | – |
aCoring method: Rumohr coring (RC), gravity coring (GC), or manually pushed cores (PC).
bIn parentheses, number of cycles needed for successful amplification.
cNumber of clones that resulted in sequences >800 nucleotides after quality check and removing the vector sequence.
dThe number of OTUs and coverage were defined at a cutoff of 5% amino acid sequence difference.
eTwo different depth intervals (SKA51, SKA52) were analyzed at station SKA5.
fSamples from stations M5, BB, LF1, and LF4 were sampled for hydrocarbon gas analyses only.
gReplicate sediment cores (LF1-6) were taken in a seepage area in Limfjorden and analyzed separately for hydrocarbon gasses (2) and molecular signatures (4).
++, strong amplicon with the correct product size. +, weak amplicon with the correct product size. -, no amplicon obtained at a maximum of 55 cycles. n.a., not analyzed.