Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)
Abstract
:Introduction
Material and Methods
Site Description and Treatment Unit
Isolation and Characterization of GAC Bacteria
Functional Gene Array Analysis of the Biofilm Communities
Results and Discussion
Chemical and Physical Analysis of Reactor Performance
Characterization of GAC Microbial Community
Functional Gene Array of GAC Microbial Community Samples
- (i)
- Cell density determined by microscopical observations and indirect cell counts increased coincident with nutrient uptake, indicating that growth was occurring.
- (ii)
- Almost 96% of all isolated cultures were capable of utilizing diesel compounds as sole carbon and energy source.
- (iii)
- Uptake of oxygen, nitrate and sulfate were indicative of both aerobic and anaerobic respiration activity.
- (iv)
- Probe hybridization patterns indicated that aerobic, denitrifying, and sulfate- and iron-reducing bacteria were present within the biofilm community.
- (v)
- A highly diverse with a broad catabolic potential and stable community was selected early within the treatment unit as determined by FGAs.
1Parameter | Influent FBR unit | Effluent FBR unit | ||||
---|---|---|---|---|---|---|
Day 61 | Day 153 | Day 212 | Day 61 | Day 153 | Day 212 | |
TPH (mg/L) | 554.3 | 1064.9 | 999.8 | 9.4 | 32.0 | 6.9 |
DO (mg/L) | 6.58 | 3.06 | 3.60 | - | 1.42 | 1.57 |
Turbidity (NTU) | 66 | 446 | 150 | 15 | 999 | 21 |
N-NH3 (mg/L) | 1.35 | 4.80 | 0.13 | 1.56 | 6.60 | 0.27 |
N-NO3 (mg/L) | 6.7 | 19.9 | 0.8 | 4.8 | 7.8 | 0.6 |
S-SO4 (mg/L) | - | 16.7 | 18.2 | - | 7.0 | 1.7 |
Gene arrays | % Similarity | ||
---|---|---|---|
Day 30 | Day 61 | Day 153 | |
Day 61 | 47.5 | - | - |
Day 153 | 49.6 | 74.4 | - |
Day 212 | 61.4 | 69.8 | 73.8 |
Probe Category | Total Gene Probe Number | Total Hybridized Probes | Gene ID Category |
---|---|---|---|
Metabolic Genes (C, N, S cycles) | 5,769 | 333 | Geobacter sp. cytochrome family, nirS, nirK, nifH, nosZ, amoA, pmo, pmoA, dsrA, dsrB |
Organic Degradation | 4,014 | 270 | Nitrobenzene, naphthalene, biphenyl, 2,4-D, MTBE, toluene, nitroluene |
Metal Resistance | 2,402 | 172 | Mercury, copper, arsenic, nickel, cobalt, cadmium |
Total Genes | 12,185 | 775 |
Gene Name | Gene Description/Source/Gene ID | 1Signal Noise Ratio | |||
---|---|---|---|---|---|
Day 30 | Day 61 | Day 153 | Day 212 | ||
Phthalate | Putative phthalate ester hydrolase/Arthrobacter keyseri/13242052_108 | 13.28 (7.73) | 3.38 (1.31) | 7.65 (0.61) | 12.41 (12.91) |
Phthalate | Phthalate dioxygenase large subunit/Arthrobacter keyseri/13242054_353 | 4.83 (2.23) | 4.31 (1.34) | 9.57 (1.56) | 7.60 (4.66) |
Phthalate | 3,4-dihydroxyphthalate 2-decarboxylase/Arthrobacter keyseri/13242058_587 | 5.33 (1.53) | 3.90 (1.41) | 12.01 (0.59) | 6.85 (2.51) |
MTBE | Alkane 1-monooxygenase/Pseudomonas fluorescens/13445194_108 | 3.44 (1.38) | 3.69 (1.45) | 9.76 (0.39) | 4.34 (1.73) |
Benzoate/anaerobic | Thiolase (acetyl-CoA acetyltransferase)/Bacillus halodurans C-125/15614592_1076 | 4.71 (2.59) | 4.39 (2.03) | 10.71 (1.14) | 4.83 (1.49) |
Thiocyanate | Carbon monoxide dehydrogenase/Sulfolobus solfataricus P2/15898062_686 | 4.29 (1.56) | 4.64 (1.86) | 9.08 (0.91) | 5.47 (2.64) |
Phthalate | phthalate permease/Sulfolobus tokodaii str. 7/15922956_410 | 9.37 (5.65) | 2.82 (1.14) | 4.03 (0.60) | 19.55 (12.12) |
Protocatechuate | Protocatechuate 3,4-dioxygenase, alpha subunit/Caulobacter crescentus/16126648_384 | 2.94 (1.01) | 6.59 (3.99) | 20.30 (2.24) | 13.90 (11.30) |
Protocatechuate | Putative protocatechuate 3,4-dioxygenase/Sinorhizobium meliloti 1021/16265236_532 | 3.37 (1.32) | 11.62 (6.23) | 31.43 (1.86) | 12.51 (7.28) |
Biphenyl | Biphenyl dioxygenase/Ralstonia eutropha/1890342_658 | 5.46 (2.27) | 2.31 (0.67) | 3.65 (0.60) | 7.22 (4.97) |
Aniline | Aniline dioxygenase beta-subunit/Acinetobacter sp. YAA/2627148_399 | 3.14 (1.57) | 3.57 (1.39) | 5.33 (0.71) | 4.23 (1.41) |
Protocatechuate | 3,4-dioxygenase beta chain/Bradyrhizobium japonicum USDA 110/27:31794411_472 | 5.11 (1.33) | 4.04 (1.52) | 9.51 (1.06) | 6.13 (2.88) |
Cyclohexanol | Cyclohexanone monooxygenase/Bradyrhizobium japonicum USDA 110/27382095_773 | 4.44 (1.76) | 4.24 (1.73) | 9.32 (0.82) | 6.40 (2.90) |
Phthalate | 3,4-dihydroxy-3,4-dihydrophthalate dehydrogenase/Terrabacter sp./27531096_403 | 4.44 (2.33) | 6.35 (3.73) | 6.63 (0.82) | 4.25 (1.59) |
Toluene/anaerobic | Benzylsuccinate synthase gamma subunit/Thauera aromatica/3184130_28 | 6.26 (1.97) | 5.40 (2.11) | 15.41 (0.96) | 7.98 (2.23) |
Acetylene | Probable ephA protein/Pirellula sp. 1/32473431_370 | 4.39 (1.97) | 6.57 (4.21) | 11.40 (1.18) | 6.48 (2.06) |
Biphenyl | Biphenyl dihydrodiol dehydrogenase/Bacillus sp. JF8/32562914_541 | 6.86 (2.19) | 4.22 (2.41) | 16.08 (1.26) | 8.15 (2.56) |
Acetylene | Acetylene hydratase Ahy/Pelobacter acetylenicus/33325847_969 | 5.68 (2.28) | 4.27 (2.19) | 11.74 (0.91) | 6.42 (3.39) |
Protocatechuate | Putative protocatechuate 3,4 dioxygenase/marine α proteobacterium SE45/38490070_560 | 22.03 (14.05) | 11.30 (12.20) | 38.79 (13.74) | 8.89 (4.81) |
Thiocyanate | ACDS complex carbon monoxide dehydrogenase/Methanopyrus kandleri/38503097_1862 | 8.40 (3.54) | 3.94 (1.47) | 5.02 (0.44) | 7.48 (5.86) |
Biphenyl | Receptor-like histidine kinase/Rhodococcus erythropolis/3868875_3209 | 12.42 (6.00) | 13.16 (13.32) | 12.20 (2.18) | 6.23 (4.32) |
Benzoate/anaerobic | Ferredoxin, 2Fe-2S/uncultured bacterium 580/40063438_226 | 3.43 (0.79) | 3.18 (1.31) | 6.46 (1.06) | 4.70 (2.71) |
Benzoate/anaerobic | Ferredoxin/Desulfotomaculum thermocisternum/4028019_136 | 3.26 (0.70) | 2.93 (1.07) | 4.54 (0.59) | 5.98 (2.73) |
Thiocyanate | Carbon monoxide dehydrogenase/Thermoproteus tenax/41033719_176 | 4.47 (1.47) | 3.65 (1.36) | 8.93 (0.86) | 6.01 (2.91) |
Acknowledgements
References
- Bertrand, J. C.; Caumette, P.; Mille, G.; Gilewicz, M.; Denis, M. Anaerobic biodegradation of hydrocarbons. Sci. Prog 1989, 73, 333–50. [Google Scholar]
- Da Silva, M.; Alvarez, L. B.; Alvarez, P. J. Enhanced anaerobic biodegradation of benzene- toluene- ethylbenzene- xylene-ethanol mixtures in bioaugmented aquifer columns. Appl. Environ. Microbiol 2004, 70, 4720–4726. [Google Scholar]
- Davey, M. E.; O’Toole, G. A. Microbial biofilms: from ecology to molecular genetics. Microbiol. Mol. Biol. Rev 2000, 64, 847–867. [Google Scholar]
- Dojka, M. A.; Hugenholtz, P.; Haack, S. K.; Pace, N. R. Microbial diversity in hydrocarbon-and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 1998, 64, 3869–3877. [Google Scholar]
- Hatzinger, P. B.; Greene, M. R.; Frisch, S.; Togna, A. P.; Manning, J.; Guarini, W. J. Biological treatment of perchlorate-contaminated groundwater using fluidized bed reactors. 2nd International Conference on Remediation of Chlorinated and Recalcitrant Compounds, May 22–25; 2000. [Google Scholar]
- Hicks, B.; Caplan, J. Bioremediation: a natural solution. Poll. Engin 1993, 25, 30–33. [Google Scholar]
- Hollinger, C.; Zehnder, A. J. Anaerobic biodegradation of hydrocarbons. Curr. Opin. Biotechnol 1996, 7, 326–330. [Google Scholar]
- Kamnikar, B. Bioremediation of contaminated soil. Poll. Engin 1992, 24, 50–52. [Google Scholar]
- Kleikemper, J.; Schroth, M. H.; Sigler, W. V.; Schmucki, M.; Bernasconi, S. M.; Zeyer, J. Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer. Appl. Environ. Microbiol 2002, 68, 1516–1523. [Google Scholar]
- Massol-Deyá, A.; Whallon, J.; Hickey, R. F.; Tiedje, J. M. Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater. Appl. Environ. Microbiol 1995, 61, 769–777. [Google Scholar]
- Massol-Deyá, A.; Weller, R.; Ríos-Hernández, L.; Zhou, J-Z.; Hickey, R. F.; Tiedje, J. M. Succession and convergence of biofilm communities in fixed-film reactors aromatic hydrocarbons in groudwater. Appl. Environ. Microbiol. 1997, 63, 270–276. [Google Scholar]
- Ogram, A.; Sayler, G. S.; Barkay, T. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 1987, 7, 57–66. [Google Scholar]
- Rhee, S-K.; Liu, X.; Wu, L.; Chong, S. C.; Wan, X.; Zhou, J. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 2004, 70, 4303–4317. [Google Scholar]
- Rölling, W. F. M.; Milner, M. G.; Jones, D. M.; Frateprieto, F.; Swannell, R. P. J.; Daniel, F.; Head, I. M. Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Appl. Environ. Microbiol 2004, 68, 2603–2613. [Google Scholar]
- Rooney-Varga, J. N.; Anderson, R. T.; Fraga, J. L.; Ringelberg, D.; Lovley, D. R. Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl. Environ. Microbiol 1999, 65, 3056–3063. [Google Scholar]
- Schadt, C. W.; Liebich, J.; Chong, S. C.; Gentry, T. J.; He, Z.; Pan, H.; Zhou, J. Design and use of functional gene microarrays (FGA’s) for the characterization of microbial communities. Methods Microbiol 2005, 33, 331–368. [Google Scholar]
- Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J. Molecular analysis of microbial community structures in pristine and contaminated aquifers: field and laboratory microcosm experiments. Appl. Environ. Microbiol 1999, 65, 2143–2150. [Google Scholar]
- Sutton, P. M.; Mishra, P. N. Activated carbon based biological fluidized beds for contaminated water and wastewater treatment: A State-Of-The-Art-Review. Natl. Sci. Technol 1994, 29, 309–317. [Google Scholar]
- Tiquia, S. M.; Wu, L.; Chong, S. C.; Passovets, S.; Xu, D.; Xu, Y.; Zhou, J. Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 2004, 36, 664–675. [Google Scholar]
- Tolker-Nielsen, T.; Brinch, U. C.; Ragas, P. C.; Andersen, J. B.; Jacobsen, C. S.; Molin, S. Development and dynamics of Pseudomonas sp. biofilms. J. Bacteriol 2000, 182, 6482–6489. [Google Scholar]
- Watanabe, K.; Watanabe, K.; Kodama, Y.; Syutsubo, K.; Haramaya, S. Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl. Environ. Microbiol 2000, 66, 4803–4809. [Google Scholar]
- Weymann, D. Biosparging used in aquifer remediation. Poll. Engin 1995, 27, 36–41. [Google Scholar]
- Wu, L.; Liu, X.; Schadt, C. W.; Zhou, J.-Z. Microarray-based analysis of sub-nanogram quantities of microbial community DNAs using Whole Community Genome Amplification (WCGA). Appl. Environ. Microbiol 2006, 72, 4931–4941. [Google Scholar]
- Zhou, J. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol 2003, 6, 288–294. [Google Scholar]
- Zhou, J.; Bruns, M. A.; Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol 1996, 62, 316–322. [Google Scholar]
- Zhou, J.; Palumbo, A. V.; Strong, J. M. Phylogenetic characterization of a mixed-microbial community capable of degrading carbon tetrachloride. Appl. Biochem. Biotechnol 1999, 80, 243–253. [Google Scholar]
© 2006 MDPI. All rights reserved.
Share and Cite
Rodríguez-Martínez, E.M.; Pérez, E.X.; Schadt, C.W.; Zhou, J.; Massol-Deyá, A.A. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico). Int. J. Environ. Res. Public Health 2006, 3, 292-300. https://doi.org/10.3390/ijerph2006030036
Rodríguez-Martínez EM, Pérez EX, Schadt CW, Zhou J, Massol-Deyá AA. Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico). International Journal of Environmental Research and Public Health. 2006; 3(3):292-300. https://doi.org/10.3390/ijerph2006030036
Chicago/Turabian StyleRodríguez-Martínez, Enid M., Ernie X. Pérez, Christopher W. Schadt, Jizhong Zhou, and Arturo A. Massol-Deyá. 2006. "Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico)" International Journal of Environmental Research and Public Health 3, no. 3: 292-300. https://doi.org/10.3390/ijerph2006030036