Table 2. Most probable affiliation of 16S rRNA gene sequences in the biofilm cultures and the original biofilm.
| Affiliation | Biofilm cultures (proportion %) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| OB | IO | Ref300N-23C | 900N-23C | 300N-30C | 900N-30C | 0%NaCl | 0.5%NaCl | 1.0%NaCl | |||
| Ignavibacteriae; Igavibacteriales; | Ignavibacterium | 0.37 | 0.13 | 0.01 | 0.19 | 0.06 | |||||
| Tenericutes; Acholeplasmatales; | Acholeplasma | 0.05 | 0.04 | 0.05 | 0.04 | 0.52 | 0.02 | ||||
| Bacteroidetes; Flavobacteriales; | Aequorivita | 0.01 | 0.18 | 0.10 | 0.14 | 0.04 | 0.01 | 0.11 | 0.22 | ||
| ” | ” | Muricauda | 0.06 | 0.08 | 0.01 | 0.01 | 0.10 | ||||
| ” | ” | Winogradskyella | 0.28 | 4.28 | 0.10 | 0.11 | 0.15 | 0.11 | 0.20 | 0.11 | |
| Proteobacteria; | |||||||||||
| Alphaproteobacteria; Rhizobiales; | Aminobacter | 0.33 | 0.01 | 0.05 | 0.22 | ||||||
| ” | ” | Aquamicrobiuma | 11.6 | 0.46 | 0.02 | ||||||
| ” | ” | Hoeflea | 0.30 | 0.76 | 0.03 | 0.01 | 0.06 | 0.12 | 0.06 | ||
| ” | ” | Nitratireductor | 1.40 | 0.03 | |||||||
| ” | ” | Hyphomicrobiuma | 45.8 | 8.40 | 10.8 | 6.78 | 0.25 | ||||
| H. nitrativorans NL23, qPCR (cp napA/ng) | 8.7(7.2)a104 | 7.0(4.3)a104 | 1.8(1.8)a102 | 6.0(3.2)a101 | 1.3(0.5)a102 | 1.3(0.9)a102 | 2.8(1.0)a104 | 5.3(6.5)a104 | 1.1(0.9)a104 | ||
| Alphaproteobacteria; Rhodobacterales; | Litorisediminicola | 0.38 | 1.43 | ||||||||
| ” | ” | Lutimaribacter | 1.71 | 8.93 | |||||||
| ” | ” | Marinovum | 1.28 | 1.62 | |||||||
| ” | ” | Maritimibacter | 2.50 | 2.44 | 0.01 | 0.01 | |||||
| ” | ” | Oceanicola | 0.06 | 0.01 | 0.08 | 0.03 | 0.01 | ||||
| ” | ” | Paracoccusa | 0.01 | 0.07 | 0.01 | 0.02 | |||||
| ” | ” | Roseovarius | 7.32 | 8.18 | 0.01 | ||||||
| ” | ” | Stappiaa | 0.02 | 1.26 | 0.09 | 0.43 | 0.27 | 0.42 | 0.27 | 0.35 | 0.17 |
| Alphaproteobacteria; Rhodospirillales | Oceanibaculum | 12.3 | 7.36 | 0.03 | 0.01 | 0.01 | 0.20 | 0.04 | |||
| Proteobacteria; | |||||||||||
| Gammaproteobacteria; Alteromonadales | Marinobactera | 0.15 | 0.05 | 0.06 | 0.05 | 0.02 | 0.01 | 0.01 | |||
| ” | Oceanospirillales | Marinicella | 0.78 | 7.24 | 1.46 | 1.50 | 3.40 | 5.02 | 0.23 | 1.55 | 0.94 |
| ” | Pseudomonadales | Pseudomonasa | 0.09 | 0.11 | 0.04 | 0.13 | 0.52 | 0.64 | 0.80 | 0.05 | |
| ” | Thiotrichales | Methylophaga | 3.50 | 42.8 | 97.7 | 97.1 | 95.1 | 91.8 | 85.7 | 88.3 | 97.9 |
| M. nitratireducenticrescens, qPCR (cp narG1/ng) | 5.6(3.2)a103 | 5.6(4.6)a104 | 2.3(0.6)a105 | 1.9(0.5)a105 | 2.1(0.4)a105 | 2.1(1.4)a105 | 4.7(2.0)a104 | 3.6(2.7)a104 | 1.5(0.2)a105 | ||
| Others | 9.86 | 4.27 | 0.25 | 0.37 | 0.53 | 2.00 | 2.28 | 0.69 | 0.25 | ||
| Total of reads | 348,358 | 319,265 | 9,610 | 14,048 | 8,532 | 13,915 | 13,800 | 9,375 | 12,560 | ||
Notes.
The V1–V3 regions of the 16S rRNA gene sequences were amplified and sequenced by pyrosequencing except for the OB and IO samples from which the V6–V8 regions were sequenced by Illumina (see Document S2 for complete analysis and sequences).
- OB
- Original biofilm
In grey: qPCR results are from Payette et al. (2019), with standard deviation values under parentheses of triplicate cultures. narG1 used in qPCR for M. nitratireducenticrescens cannot discriminate strain JAM1 and strain GP59 (identical sequences between the two).
a
Identified genus with species that were reported involved in denitrification.