Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture
Abstract
:1. Introduction
2. Materials and Methods
2.1. Culture Establishment
2.2. Metabolite Analysis and 13C-bicarbonate Tracer Experiments
2.3. Microbial Community Analysis and Targeted Functional Gene Analysis
2.4. 13C-Naphthalene Stable Isotope Probing
2.5. Metagenomic Sequencing, Binning, and Genomic Annotation
3. Results and Discussion
3.1. Analytical Evidence of Methanogenic Naphthalene Degradation
3.2. Detection of Putative Naphthalene Metabolites
3.3. Pinpointing Putative Naphthalene Degraders Using Pyrosequencing and DNA-SIP
3.4. Metagenomic Evidence Predicts Clostridiaceae to Be a Key Naphthalene Degrader in NDC
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Taxon | 13C Heavy | 12C Control | 13C Light |
---|---|---|---|
Archaea | |||
Methanosaeta | 1.49 | 5.18 | 4.83 |
Methanobacterium | 0.14 | 0.64 | 2.19 |
Methanoculleus | 0.72 | 0.17 | 0.04 |
Thermoplasmata WCHA-57 | 0.00 | 0.04 | 0.35 |
Bacteroidetes | |||
Proteiniphilum | 0.07 | 0.53 | 0.30 |
Rikenellaceae vadinBC27 | 0.00 | 0.17 | 0.70 |
Chloroflexi | |||
Anaerolineaceae | 0.14 | 1.48 | 0.73 |
Firmicutes | |||
Clostridiaceae | 14.5 | 17.8 | 4.98 |
Sedimentibacter | 0.07 | 1.59 | 0.47 |
Clostridium | 0.27 | 0.07 | 0.03 |
Peptococcaceae | 0.16 | 0.13 | 0.01 |
Proteobacteria | |||
Desulfuromonadales | 68.5 | 61.6 | 81.0 |
Geobacter | 1.88 | 1.70 | 2.06 |
Desulfuromonas | 0.45 | 1.68 | 0.36 |
Desulfobulbus | 0.32 | 0.42 | 0.54 |
Desulfovibrio | 0.43 | 0.44 | 0.11 |
Deltaproteobacteria | 0.41 | 0.15 | 0.21 |
Genome1 IMG ID | Genome1 Name | Genome Size, bp (Assembled) | Gene Count (Assembled) | Genome2 IMG ID | Genome2 Name | ANI 1→2 | ANI 2→1 | AF 1→2 | AF 2→1 | Total BBH |
---|---|---|---|---|---|---|---|---|---|---|
2724679725 | Anaerolinea sp. Bin 1 | 2333788 | 2249 | 649633005 | Anaerolinea thermophila UNI-1 | 67.6 | 67.6 | 0.08 | 0.05 | 221 |
2724679726 | Anaerolinea sp. Bin 2 | 2271625 | 2153 | 649633005 | Anaerolinea thermophila UNI-1 | 67.7 | 67.7 | 0.13 | 0.08 | 318 |
2724679696 | Unclassified Clostridiaceae sp. Bin 1 | 5438132 | 5424 | 2582580929 | Youngiibacter fragilis | 87.5 | 87.5 | 0.54 | 0.75 | 2904 |
2724679721 | Desulfovibrio sp. Bin 1 | 3088242 | 2959 | 2561511137 | Desulfovibrio alcoholivorans DSM 5433 | 72.6 | 72.7 | 0.40 | 0.25 | 1337 |
2724679697 | Unclassified Desulfuromonadales sp. Bin 1 | 4390079 | 4104 | 640427115 | Geobacter uraniireducens Rf4 | 72.4 | 72.4 | 0.29 | 0.25 | 1225 |
2724679723 | Unclassified Desulfuromonadales sp. Bin 2 | 3876684 | 3546 | 640427115 | Geobacter uraniireducens Rf4 | 72.2 | 72.2 | 0.35 | 0.26 | 1230 |
2724679724 | Unclassified Desulfuromonadales sp. Bin 3 | 2526538 | 2519 | 642555130 | Geobacter lovleyi SZ | 77.0 | 77.0 | 0.69 | 0.43 | 1737 |
2724679722 | Methanosaeta sp. Bin 1 | 2683322 | 2798 | 650716054 | Methanosaeta concilii GP-6 | 96.6 | 96.6 | 0.81 | 0.76 | 2209 |
2724679727 | Sphaerochaeta sp. Bin 1 | 1750954 | 1956 | 650377973 | Sphaerochaeta globosa Buddy | 80.5 | 80.5 | 0.70 | 0.37 | 1321 |
2724679720 | Unclassified Rhodospirillales Bin 1 | 3473168 | 3651 | 2651870079 | Unclassified Rhodospirillaceae Bin 35 | 69.5 | 69.5 | 0.15 | 0.14 | 546 |
Gene ID | IMG Predicted Protein Annotation | Length (aa) | NaphS2 Ortholog | Locus | % Identity (% Similarity) | Best BLASTP Ortholog | Accession No. | % Identity (% Similarity) |
---|---|---|---|---|---|---|---|---|
2727804033 | Hypothetical protein | 60 | N/A | - | - | hypothetical protein [Clostridiales bacterium VE202-03] | WP_024723634 | 43 (71) |
2727804034 | Crotonobetainyl-CoA:carnitine CoA-transferase CaiB | 412 | CoA-transferase family III protein | NPH_4605 NPH_6726 NPH_5274 | 31 (50) 24 (46) 27 (44) | Formyl-coenzyme A transferase [uncultured Clostridium sp.] | SCJ80195 | 55 (74) |
2727804035 | acetyl-CoA C-acetyltransferase | 387 | Acetyl-CoA C-acyltransferase | NPH_3581 NPH_6994 NPH_6993 NPH_5273 | 43 (61) 43 (62) 38 (62) 38 (55) | MULTISPECIES: acetyl-CoA acetyltransferase [Geobacillus] | WP_074043744 | 51 (69) |
2727804036 | 3-hydroxybutyryl-CoA dehydrogenase | 288 | 3-hydroxybutyryl-CoA dehydrogenase | NPH_5812 NPH_5906 NPH_5896 NPH_7219 | 38 (58) 40 (56) 36 (53) 34 (53) | 3-hydroxyacyl-CoA dehydrogenase [Clostridiales bacterium PH28_bin88] | KKM10089 | 53 (71) |
2727804037 | H+/gluconate symporter | 444 | N/A | - | - | MULTISPECIES: hypothetical protein [Clostridiales] | WP_007862308 | 43 (65) |
2727804038 | enoyl-[acyl-carrier protein] reductase II | 315 | 2-nitropropane dioxygenase | NPH_5508 NPH_6957 | 35 (52) 33 (53) | 2-nitropropane dioxygenase [Anaerosporomusa subterranea] | WP_066237624 | 52 (70) |
2727804039 | Enoyl-CoA hydratase/isomerase | 85 | 3-hydroxybutyryl-CoA dehydratase | NPH_5887 NPH_5907 | 47 (61) 40 (56) | MULTISPECIES: 3-hydroxybutyryl-CoA dehydratase [Clostridiales] | WP_007862300 | 52 (74) |
2727804040 | Enoyl-CoA hydratase/isomerase | 78 | 3-hydroxybutyryl-CoA dehydratase | NPH_6695 NPH_5897 NPH_5898 | 39 (62) 38 (63) 45 (65) | enoyl-CoA hydratase [Desulfotomaculum thermosubterraneum] | WP_072869855 | 55 (77) |
2727804041 | 2-nitropropane dioxygenase precursor | 321 | 2-nitropropane dioxygenase | NPH_6957 NPH_5508 | 38 (60) 31 (48) | nitronate monooxygenase [Clostridium citroniae] | WP_083424018 | 71 (84) |
2727804042 | Crotonobetainyl-CoA:carnitine CoA-transferase CaiB | 409 | CoA-transferase family III protein | NPH_4605 NPH_1868 | 34 (52) 26 (44) | MULTISPECIES: CoA transferase [Clostridiales] | WP_007862305 | 48 (68) |
2727804043 | 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase | 262 | putative enoyl-CoA hydratase | NPH_0885 NPH_5898 NPH_5897 | 31 (50) 32 (54) 32 (52) | enoyl-CoA hydratase [Enterococcus silesiacus] | WP_071879306 | 47 (71) |
2727804044 | Hypothetical protein | 25 | N/A | - | - | ATP-dependent endonuclease [Bacillus cereus] | OPA11549 | 72 (77) |
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Toth, C.R.A.; Berdugo-Clavijo, C.; O’Farrell, C.M.; Jones, G.M.; Sheremet, A.; Dunfield, P.F.; Gieg, L.M. Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms 2018, 6, 65. https://doi.org/10.3390/microorganisms6030065
Toth CRA, Berdugo-Clavijo C, O’Farrell CM, Jones GM, Sheremet A, Dunfield PF, Gieg LM. Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms. 2018; 6(3):65. https://doi.org/10.3390/microorganisms6030065
Chicago/Turabian StyleToth, Courtney R. A., Carolina Berdugo-Clavijo, Corynne M. O’Farrell, Gareth M. Jones, Andriy Sheremet, Peter F. Dunfield, and Lisa M. Gieg. 2018. "Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture" Microorganisms 6, no. 3: 65. https://doi.org/10.3390/microorganisms6030065
APA StyleToth, C. R. A., Berdugo-Clavijo, C., O’Farrell, C. M., Jones, G. M., Sheremet, A., Dunfield, P. F., & Gieg, L. M. (2018). Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms, 6(3), 65. https://doi.org/10.3390/microorganisms6030065