Bacterial Isolates from Greek Sites and Their Efficacy in Degrading Petroleum
Abstract
:1. Introduction
2. Materials and Methods
2.1. Soil Sampling and Media
2.2. Isolation of Oil Hydrocarbon Degraders
2.3. Phenotypical Characterization of Bacterial Isolates
2.4. Isolation of Genomic DNA and Detection of the 16S rDΝA Gene, Catechol 2,3-Dioxygenase Enzyme (nahH) Gene and Aliphatic Alcohol Dehydrogenase Enzyme (alkJ) Gene
2.5. Estimation of Biodegradation Activity in Batch Cultures
2.6. Analysis of Petroleum Hydrocarbons in Crude Oil and Liquid Naphthalene Cultures
3. Results
3.1. Physicochemical Parameters of the Sampling Sites
3.2. Determination of Polycyclic Aromatic Hydrocarbons (PAHs) at the Sampling Sites
3.3. Bacterial Strains Displaying Petroleum-Degrading Ability
3.4. Presence of Petroleum-Hydrocarbon-Degrading Genes alkJ and nahH in the Specific Bacterial Strains
3.5. Growth of Isolated Bacterial Strains in Crude Oil or Naphthalene Batch Cultures
3.6. Patterns of Biodegradability of Specific Bacterial Strains
3.7. Development of Consortia for Crude Oil Degradation
3.8. Alkanes/Hopanes Ratio during Crude Oil Degradation by Pseudomonas plecoglossicida
4. Discussion
4.1. Physicochemical Parameters of Sampling Sites and Microbial Diversity
4.2. Occurrence of alkJ and nahH Genes in Bacteria Populations Is Correlated with the Level of Contamination
4.3. Bacterial Population Diversity in Contaminated Sites
4.4. Cometabolism of Hydrocarbons by Microbial Community and Consortia Development
4.5. Selection of a Specific Strain and Its Potential Use in Autochthonous Bioaugmentation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Physicochemical Parameter | Keri Lake | Glyfada Beach |
---|---|---|
pH | 8.5 | 8.0 |
Temperature | 19.0 °C | 22.0 °C |
Salinity | 6.9 ppt * | 37.8 ppt * |
Dissolved Oxygen | 10.1 mg/L | 8.5 mg/L |
Sampling Site | Naphthalene (NAPH) | Anthracene (ANTH) | Fluoranthene (FLUO) | Benzo(b) Fluoranthene (B[b]F) | Benzo(k) Fluoranthene (B[k]F) | Benzo(a) Pyrene (B[a]P) | Benzo(ghi) Perylene (B[ghi]P) | Indeno (1,2,3-cd) Pyrene (IP) |
---|---|---|---|---|---|---|---|---|
Sampling Site 1 Glyfada Beach A | 8.63 | 0.55 | 7.01 | 46 | 7.36 | 22.4 | 7.16 | 5.69 |
Sampling Site 2 Glyfada Beach B | 3.3 | 32.2 | 79.7 | 122 | 17 | 60 | 19.2 | 7.27 |
Sampling Site 3 Glyfada Beach C | NT * | NT * | NT * | <LOQ ** | NT * | NT * | NT * | NT * |
Sampling Site 4 Keri Lake D | 9 | 35.7 | 75.5 | 131 | 17 | 62 | 17.8 | 7.51 |
Sampling Site | Total Isolated Bacterial Strains | Strains with Ability to Degrade Crude Oil | Strains with alkJ Gene | Strains with nahH Gene | Strains with Both Genes Present |
---|---|---|---|---|---|
Sampling Site 1 Glyfada Beach A | 19 | 16 (84.21%) | 7 (46.7%) | 9 (60.0%) | 2(12.5%) |
Sampling Site 2 Glyfada Beach B | 15 | 11 (73.33%) | 7 (63.6%) | 7 (63.6%) | 5 (45.5%) |
Sampling Site 3 Glyfada Beach C | 31 | 4 (12.9%) | 1 (25.0%) | 3 (75.0%) | 1 (25.0%) |
Sampling Site 4 Keri Lake D | 8 | 7 (87.5%) | 5 (71.4%) | 4 (54.1%) | 2 (28.6%) |
ATHUBA Culture Collection | - | 10 | 4 (40.0%) | 4 (40.0%) | 2 (20.0%) |
Sampling Site | Strain Name and Classification | Biodegradability Percentage of Crude Oil (%) | Biomass (g/L) of Crude Oil | Biomass (g/L) of Naphthalene |
---|---|---|---|---|
Sampling Site 1 | Streptomyces flavoviridis, ATHUBA 682 | 25.80 ± 0.69 | 0,11 ± 0,03 | 0.10 ± 0.02 |
Streptomyces aridus, ATHUBA 683 | 27.80 ± 1.01 | 0.44 ± 0.05 | 0.21 ± 0.01 | |
Staphylococcus sp., ATHUBA 684 | 30.40 ± 0.99 | 0.38 ± 0.04 | 0.27 ± 0.02 | |
Isoptericola chiayiensis, ATHUBA 685 | 23.40 ± 0.65 | 0.19 ± 0.02 | 0.11 ± 0.01 | |
Isoptericola chiayiensis, ATHUBA 686 | 38.70 ± 1.21 | 0.34 ± 0.03 | 0.28 ± 0.01 | |
Bacillus wiedmannii sp., ATHUBA 687 | 57.70 ± 0.36 | 0.61 ± 0.04 | 0.41 ± 0.02 | |
Staphylococcus warneri, ATHUBA 688 | 32.10 ± 0.51 | 0.19 ± 0.01 | 0.17 ± 0.01 | |
Streptomyces sp., ATHUBA 689 | 66.10 ± 0.56 | 0.49 ± 0.04 | 0.42 ± 0.02 | |
Paenibacillus polymyxa, ATHUBA 690 | 40.00 ± 2.30 | 0.12 ± 0.01 | 0.09 ± 0.01 | |
Bacillus flexus, ATHUBA 691 | 60.80 ± 1.14 | 0.67± 0.05 | 0.47 ± 0.02 | |
Isoptericola chiayiensis, ATHUBA 692 | 33.00 ± 0.39 | 0.13 ± 0.01 | 0.06 ± 0.01 | |
Bacillus sp., ATHUBA 693 | 35.50 ± 0.69 | 0.11 ± 0.02 | 0.05 ± 0.01 | |
Isoptericola sp., ATHUBA 694 | 45.50 ± 1.00 | 0.22 ± 0.02 | 0.10 ± 0.01 | |
Bacillus sp., ATHUBA 695 | 40.20 ± 1.27 | 0.16 ± 0.02 | 0.12 ± 0.01 | |
Brevundimonas sp., ATHUBA 696 | 38.70 ± 1.91 | 0.21 ± 0.01 | 0.13 ± 0,01 | |
Isoptericola chiayiensis, ATHUBA 697 | 52.00 ± 1.36 | 0.66 ± 0.04 | 0.25 ± 0.01 | |
Sampling Site 2 | Streptomyces sp.,ATHUBA 698 | 45.60 ± 0.98 | 0.64 ± 0.04 | 0.41 ± 0.02 |
Halomonas lionensis, ATHUBA 699 | 27.00 ± 0.87 | 0.14 ± 0.01 | 0.14 ± 0.01 | |
Halomonas quamarina, ATHUBA 700 | 50.00 ± 1.03 | 0.41 ± 0.03 | 0.39 ± 0.02 | |
Isoptericola chiayiensis, ATHUBA 701 | 37.50 ± 1.63 | 0.27 ± 0.01 | 0.38 ± 0.02 | |
Isoptericola halotolerans, ATHUBA 702 | 14.50 ± 0.62 | 0.19 ± 0.02 | 0.21 ± 0.01 | |
Isoptericola rhizophila, ATHUBA 703 | 43.20 ± 0.28 | 0.10 ± 0.01 | 0.12 ± 0.01 | |
Isoptericola chiayiensis, ATHUBA 704 | 28.80 ± 1.35 | 0.15 ± 0.01 | 0.12 ± 0.01 | |
Bacillus sp., ATHUBA 705 | 21.00 ± 1.28 | 0.37 ± 0.02 | 0.30 ± 0.02 | |
Streptomyces flavoviridis, ATHUBA 706 | 51.10 ± 1.87 | 0.49 ± 0.02 | 0.41 ± 0.02 | |
Pseudomonas plecoglossicida, ATHUBA 707 | 76.70 ± 1.23 | 0.73 ± 0.04 | 0.66 ± 0.04 | |
Paenibacillus abyssi, ATHUBA 708 | 69.30 ± 0.99 | 0.53 ± 0.03 | 0.48 ± 0.03 | |
Sampling Site 3 | Bacillus cereus, ATHUBA 709 | 37.80 ± 0.68 | 0.10 ± 0.01 | 0.05 ± 0.01 |
Bacillus sp., ATHUBA 710 | 21.10 ± 2.01 | 0.15 ± 0.01 | 0.09 ± 0.01 | |
Halomonas sp., ATHUBA 711 | 10.80 ± 1.27 | 0.15 ± 0.01 | 0.12 ± 0.01 | |
Bacillus sp., ATHUBA 712 | 10.00 ± 0.36 | 0.19 ± 0.02 | 0.13 ± 0.01 | |
Sampling Site 4 | Pseudomonas wadenswilerensis, ATHUBA 713 | 46.70 ± 0.87 | 0.47 ± 0.04 | 0.48 ± 0.03 |
Pseudomonas sp., ATHUBA 714 | 29.10 ± 0.61 | 0.23 ± 0.01 | 0.31 ± 0.02 | |
Halomonas sp., ATHUBA 715 | 27.80 ± 0.53 | 0.25 ± 0.01 | 0.19 ± 0.01 | |
Kocuria arsenatis, ATHUBA 716 | 61.30 ± 1.41 | 0.88 ± 0.05 | 0.75 ± 0.5 | |
Brevundimonas vesiculari, ATHUBA 717 | 59.20 ± 1.18 | 0.71 ± 0.05 | 0.79 ± 0.06 | |
Pseudomonas flavescens, ATHUBA 718 | 52.10 ± 1.39 | 0.68 ± 0.04 | 0.56 ± 0.04 | |
Bacillus sp., ATHUBA 719 | 38.70 ± 0.97 | 0.27 ± 0.01 | 0.31 ± 0.2 | |
ATHUBA | Streptomyces griseus, ATHUBA 720 | 25.20 ± 0.67 | 0.32 ± 0.02 | 0.13 ± 0.01 |
Culture | Streptomyces chromofuscus, ATHUBA 721 | 18.20 ±0.57 | 0.41 ± 0.03 | 0.32 ± 0.4 |
Collection | Streptomyces lividans, ATHUBA 722 | 21.90 ± 0.61 | 0.47 ± 0.02 | 0.45 ± 0.04 |
Streptomyces rochei, ATHUBA 723 | 24.00 ± 0.32 | 0.60 ± 0.04 | 0.35 ± 0.02 | |
Streptomyces griseus, ATHUBA 724 | 25.20 ± 0.32 | 0.83 ± 0.06 | 0.66 ± 0.05 | |
Nitratireductor aquamarina, ATHUBA 725 | 50.80 ± 1.25 | 0.27 ± 0.01 | 0.15 ± 0.01 | |
Thalassospira sp., ATHUBA 726 | 47.00 ± 1.10 | 0.50 ± 0.04 | 0.47 ± 0.03 | |
Pseudomonas plecoglossicida, ATHUBA 727 | 60.10 ± 1.38 | 0.73 ± 0.05 | 0.27 ± 0.01 | |
Nitratireductor sp., ATHUBA 728 | 41.50 ± 0.99 | 0.28 ± 0.01 | 0.28 ± 0.02 | |
Pseudomonas sp., ATHUBA 729 | 40.00 ± 0.87 | 0.80 ± 0.06 | 0.45 ± 0.03 |
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Ntroumpogianni, G.C.; Giannoutsou, E.; Karagouni, A.D.; Savvides, A.L. Bacterial Isolates from Greek Sites and Their Efficacy in Degrading Petroleum. Sustainability 2022, 14, 9562. https://doi.org/10.3390/su14159562
Ntroumpogianni GC, Giannoutsou E, Karagouni AD, Savvides AL. Bacterial Isolates from Greek Sites and Their Efficacy in Degrading Petroleum. Sustainability. 2022; 14(15):9562. https://doi.org/10.3390/su14159562
Chicago/Turabian StyleNtroumpogianni, Georgia C., Eleni Giannoutsou, Amalia D. Karagouni, and Alexandros L. Savvides. 2022. "Bacterial Isolates from Greek Sites and Their Efficacy in Degrading Petroleum" Sustainability 14, no. 15: 9562. https://doi.org/10.3390/su14159562