Table 1.
Taxonomic affiliation and naphthalene biodegradation potential of biofilm isolates obtained during the study
| Strain designation* | 16S rDNA accession numbers | Isolation source/type of enrichment | Nearest cultured neighbor upon 16S rRNA | Phylogenetic affiliation | bp | 16S rRNA sequence homology (%) | Naphthalene biodegradation as assessed by GC-MS (1 mg l−1) |
Presence of NDO-related 2Fe-2S genes |
|---|---|---|---|---|---|---|---|---|
| R1.1_4 | MN197554 | Aerobic 1st week | Pseudomonas silesiensis A3(T) | Gammaproteobacteria | 1422 | 99.7 | + | + |
| R1.1_5 | MN197555 | Aerobic 1st week | Acidovorax delafieldii DSM 64(T) | ¥Gammaproteobacteria | 1413 | 99.7 | + | + |
| R1.1_7 | MN197556 | Aerobic 1st week | Pseudomonas arsenicoxydans CECT 7543(T) | Gammaproteobacteria | 1440 | 99.2 | + | + |
| RN1.1_1 | MN197557 | Aerobic 1st week | Pseudomonas silesiensis A3(T) | Gammaproteobacteria | 1442 | 99.6 | − | − |
| RN1.1_3 uj | MN197558 | Aerobic 1st week | Pseudomonas silesiensis A(T) | Gammaproteobacteria | 1431 | 99.9 | + | + |
| RN1.1_4F | MN197559 | Aerobic 1st week | Rhodococcus jostii DSM 44719(T) | Actinobacteria | 1416 | 99.9 | + | − |
| RN1.1_5 | MN197560 | Aerobic 1st week | Pseudomonas silesiensis A(T) | Gammaproteobacteria | 1475 | 99.3 | + | + |
| RN1.1_7 | MN197561 | Aerobic 1st week | Massilia aurea AP13(T) | ¥Gammaproteobacteria | 1358 | 99.0 | − | − |
| BGN1.1_2 | MN197562 | Aerobic 1st week | Acidovorax facilis CCUG 2113(T) | ¥Gammaproteobacteria | 1355 | 99.6 | − | − |
| BGN1.1_3 | MN197563 | Aerobic 1st week | Acidovorax delafieldii DSM 64(T) | ¥Gammaproteobacteria | 1364 | 99.5 | + | − |
| BGN1.1_4 | MN197564 | Aerobic 1st week | Acidovorax delafieldii DSM 64(T) | ¥Gammaproteobacteria | 1432 | 99.9 | + | − |
| BGN1.1_5 | MN197565 | Aerobic 1st week | Rhodococcus jostii DSM 44719(T) | Actinobacteria | 1407 | 99.6 | + | − |
| BGN1.1_6 | MN197566 | Aerobic 1st week | Pseudomonas mandelii NBRC 103147(T) | Gammaproteobacteria | 1355 | 99.7 | + | + |
| BGN1.1_8 | MN197567 | Aerobic 1st week | Rhodococcus jostii DSM 44719(T) | Actinobacteria | 1393 | 99.8 | + | − |
| R3.6_1 | MN197568 | Aerobic 6e week | Pseudomonas umsongensis DSM 16611(T) | Gammaproteobacteria | 1430 | 99.7 | − | − |
| R3.6_2 | MN197569 | Aerobic 6th week | Pseudomonas umsongensis DSM 16611(T) | Gammaproteobacteria | 1438 | 99.5 | + | + |
| R3.6_3 | MN197570 | Aerobic 6th week | Pseudomonas laurylsulfatiphila AP3_16(T) | Gammaproteobacteria | 1376 | 99.4 | + | + |
| R3.6_4 | MN197571 | Aerobic 6th week | Pseudomonas laurentiana GSL-010(T) | Gammaproteobacteria | 1439 | 99.6 | + | + |
| RN3.6_1 | MN197572 | Aerobic 6th week | Pseudomonas umsongensis DSM 16611(T) | Gammaproteobacteria | 1446 | 99.0 | − | − |
| RN3.6_3 | MN197573 | Aerobic 6th week | Pseudomonas laurentiana GSL-010(T) | Gammaproteobacteria | 1436 | 99.2 | + | + |
| RN3.6_4 | MN197574 | Aerobic 6th week | Pseudomonas silesiensis A3(T) | Gammaproteobacteria | 1425 | 99.8 | − | − |
| BGN3.6_1 | MN197575 | Aerobic 6th week | Pseudomonas umsongensis DSM 16611(T) | Gammaproteobacteria | 1425 | 99.9 | − | − |
| BGN3.6_2 | MN197576 | Aerobic 6th week | Pseudomonas reidholzensis CCOS 865(T) | Gammaproteobacteria | 1437 | 99.5 | − | − |
| BGN3.6_3 | MN197577 | Aerobic 6th week | Pseudomonas frederiksbergensis JAJ28(T) | Gammaproteobacteria | 1434 | 99.5 | + | + |
| BGN3.6_4 | MN197578 | Aerobic 6th week | Pseudomonas umsongensis DSM 16611(T) | Gammaproteobacteria | 1438 | 99.9 | + | + |
| BGN3.6_5 | MN197579 | Aerobic 6th week | Pseudomonas laurentiana GSL-010(T) | Gammaproteobacteria | 1352 | 99.3 | + | + |
| BGN3.6_6 | MN197580 | Aerobic 6th week | Pseudomonas frederiksbergensis JAJ28(T) | Gammaproteobacteria | 1441 | 99.5 | + | + |
| HR1.1_1 | MN197581 | Oxygen-limited 2nd week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1433 | 99.8 | + | + |
| HR1.1_2 | MN197582 | Oxygen-limited 2nd week | Pseudomonas laurentiana GSL-010(T) | Gammaproteobacteria | 1432 | 99.6 | + | + |
| HR1.1_5 | MN197583 | Oxygen-limited 2nd week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1384 | 99.8 | + | + |
| HBGN1.1_3 | MN197584 | Oxygen-limited 2nd week | Pseudomonas laurentiana GSL-010(T) | Gammaproteobacteria | 1429 | 99.6 | + | + |
| HBGN1.1_4 | MN197585 | Oxygen-limited 2nd week | Achromobacter anxifer LMG 26857 | ¥Gammaproteobacteria | 1420 | 99.9 | − | − |
| HR3.3_1 | MN197586 | Oxygen-limited 6th week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1392 | 99.6 | + | + |
| HR3.3_3 | MN197587 | Oxygen-limited 6th week | Pseudomonas marginalis ATCC 10844(T) | Gammaproteobacteria | 1360 | 99.3 | + | + |
| HR3.3_4 | MN197588 | Oxygen-limited 6th week | Pseudomonas marginalis ATCC 10844(T) | Gammaproteobacteria | 1447 | 98.7 | + | + |
| HR3.3_5 | MN197589 | Oxygen-limited 6th week | Achromobacter spanius LMG 5911(T) | ¥Gammaproteobacteria | 1430 | 99.7 | − | − |
| HRN3.3_1 | MN197590 | Oxygen-limited 6th week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1441 | 99.6 | + | + |
| HRN3.3_3 | MN197591 | Oxygen-limited 6th week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1391 | 99.4 | + | + |
| HRN3.3_4 | MN197592 | Oxygen-limited 6th week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1440 | 99.8 | + | + |
| HBGN3.3_1 | MN197593 | Oxygen-limited 6th week | Pseudomonas veronii DSM11331(T) | Gammaproteobacteria | 1438 | 99.6 | + | + |
*R—direct plating on R2A agar; RN—direct plating on R2A agar, onto which 100 μl of naphthalene suspension had been previously plated (10 mg/mL); BGN—direct plating on BBH medium solidified with gellan gum, onto which 100 μl of naphthalene suspension had been previously plated (10 mg/mL); HR, HRN, HBGN—isolates originating from the oxygen-limited enrichments; “+”—designates either naphthalene degradation as assessed by GC-MS or the possession of naphthalene-dioxygenase reductase component involved in naphthalene biodegradation as detected through CODEHOP PCR
¥Formerly classified as Betaproteobacteria, which now can be found within Gammaproteobacteria in SILVA as order Betaproteobacteriales, Parks et al. 2018