A Depth Resolved Insight into Benzoyl CoA Reductase and Benzoate Dioxygenase Gene Copy Numbers within a Marine Sediment Associated with Methane Seepage

Paul V. Flanagan, Brian P. Kelleher, Shane S. O’Reilly, Michal T. Szpak, Xavier Monteys, Paul P. Kelly, Anna N. Kulakova, Leonid A. Kulakov, Christopher C. R. Allen

Geological Survey of Ireland, Beggar’s Bush, Dublin, Ireland.
School of Biological Sciences, Queen’s University Belfast, Belfast, UK.
School of Chemical Sciences, Dublin City University, Dublin, Ireland.

DOI: 10.4236/ojms.2013.34020                

Abstract

A marine sediment core obtained from a methane seepage site off the northern coast of Irelandwas analysed, at 3 depths, for catabolic genes associated with the aerobic and anaerobic degradation of aromatic compounds. Catabolic gene copy numbers varied through the core peaking at 2.1 meters below sediment surface (mbsf)-just above the sulphate boundary. Beyond the sulphate boundary gene copy numbers fell considerably, suggesting the boundary may be a critical factor in the degradation of aromatic compounds within marine sediments. At the 2.1 mbsf depth our data also suggest that known benzoyl CoA reductase utilizing bacteria are readily detectable.

Keywords

Aromatic Compounds; qPCR; bcr; bdo

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	D. R. Lovley, “Cleaning up with Genomics: Applying Molecular Biology to Bioremediation,” Nature Reviews Microbiology, Vol. 1, No. 1, 2003, pp. 35-44. http://dx.doi.org/10.1038/nrmicro731
[2]	F. Widdel and R. Rabus, “Anaerobic Biodegradation of Saturated and Aromatic Hydrocarbons,” Current Opinion in Biotechnology, Vol. 12, No. 3, 2001, pp. 259-276. http://dx.doi.org/10.1016/S0958-1669(00)00209-3
[3]	C. D. Phelps, J. Kazumi and L. Y. Young, “Anaerobic Degradation of Benzene in BTX Mixtures Dependant on Sulphate Reduction,” FEMS Microbiology Letters, Vol. 145, No. 3, 1996, pp. 433-437. http://dx.doi.org/10.1111/j.1574-6968.1996.tb08612.x
[4]	D. Canfield, B. Thamdrup and J. W. Hansen, “The Anaerobic Degradation of Organic Matter in Danish Coastal Sediments: FE reduction, Mn Reduction and Sulfate Reduction,” Geochimica et Cosmochimica Acta, Vol. 57, No. 16, 1993, pp. 3867-3883. http://dx.doi.org/10.1016/0016-7037(93)90340-3
[5]	F. Musat and F. Widdel, “Anaerobic Degradation of Benzene by a Marine Sulphate Reducing Enrichment Culture, and Cell Hybridization of the Dominant Pylotype,” Environmental Microbiology, Vol. 10, No. 1, 2008, pp. 10-19.
[6]	M. Kube, A. Beck, A. Meyerdierks, R. Amann, R. Reinhardt and R. Rabus, “A Catabolic Gene Cluster for Anaerobic Benzoate Degradation in Methanotrophic Microbial Black Sea Mats,” Systematic and Applied Microbiology, Vol. 28, No. 4, 2005, pp. 287-294. http://dx.doi.org/10.1016/j.syapm.2005.02.006
[7]	S. Dahle, V. M. Savinov, G. G. Matishov, A. Evenset and K. Naes, “Polycyclic Aromatic Hydrocarbons (PAHs) in Bottom Sediments of the Kara Sea Shelf, Gulf of Ob and Yenisei Bay,” The Science of the Total Environment, Vol. 306, No. 1-3, 2003, pp. 57-71. http://dx.doi.org/10.1016/S0048-9697(02)00484-9
[8]	M. T. Szpak, X. Monteys, S. O’Reilly, A. J. Simpson, X. Garcia, R. L. Evans, C. C. R. Allen, D. J. McNally, D. Courtier-Murias and B. P. Kelleher, “Geophysical and Geochemical Survey of a Large Marine Pockmark on the Malin Shelf, Ireland,” Geochemistry Geophysics Geosystems, Vol. 13, No. 1, 2012, p. Q01011. http://dx.doi.org/10.1029/2011GC003787
[9]	J. Zhou, M. Bruns and J. M. Tiedje, “DNA Recovery from Soils of Diverse Composition,” Applied and Environmental Microbiology, Vol. 62, No. 2, 1996, pp. 316-322.
[10]	J. R. Marchesi, T. Sato, A. J. Weightman, T. A. Martin, J. C. Fry, S. J. Hiom and W. G. Wade, “Design and Evaluation of Useful Bacterium-Specific PCR Primers That Amplify Genes Coding for 16S rRNA,” Applied and Environmental Microbiology, Vol. 64, No. 2, 1998, pp. 795-799.
[11]	A. Del Casale, P. V. Flanagan, M. J. Larkin, C. C. R. Allen and L. A. Kulakov, “Extent and Variation of PhageBorne Bacterial 16S rRNA Gene Sequences in Wastewater Environments,” Applied and Environmental Microbiology, Vol. 77, No. 15, 2011, pp. 5529-5532. http://dx.doi.org/10.1128/AEM.00457-11
[12]	D. C. White and D. B. Ringelberg, “Signature Lipid Biomarker Analysis,” In: R. S. Burlage, R. Atlas, D. Stahl, G. Geesey and G. Sayler, Eds., Techniques in Microbial Ecology, Oxford University Press, Oxford, 1998, pp. 255-288.
[13]	H. C. Pinkart, R. Devereux and P. J. Chapman, “Rapid Separation of Microbial Lipids Using Solid Phase Extraction Columns,” Journal of Microbiological Methods, Vol. 34, No. 1, 1998, pp. 9-15. http://dx.doi.org/10.1016/S0167-7012(98)00060-8
[14]	A. Otto, C. Shunthirasingham and M. J. Simpson, “A Comparison of Plant and Microbial Biomarkers in Grassland Soils from the Prairie Ecozone of Canada,” Organic Geochemistry, Vol. 36, No. 3, 2005, pp. 425-448. http://dx.doi.org/10.1016/j.orggeochem.2004.09.008
[15]	P. D. Nichols, J. B. Guckert and D. C. White, “Determination of Monounsaturated Fatty Acid Double-Bond Position and Geometry for Microbial Monocultures and Complex Consortia by Capillary GC-MS of Their Dimethyl Disulphide Adducts,” Journal of Microbiological Methods, Vol. 5, No. 1, 1986, pp. 49-55. http://dx.doi.org/10.1016/0167-7012(86)90023-0
[16]	D. Kim, S. W. Kim, K. Y. Choi, J. S. Lee and E. Kim, “Molecular Cloning and Functional Characterization of the Genes Encoding Benzoate and P-Hydroxybenzoate Degradation by the Halophilic Chromohalobacter sp. Strain HS-2,” FEMS Microbiology Letters, Vol. 280, No. 2, 2008, pp. 235-241. http://dx.doi.org/10.1111/j.1574-6968.2008.01067.x
[17]	B. Song and B. B.Ward, “Genetic Diversity of Benzoyl Coenzyme A Reductase Genes Detected in Denitrifying Isolates and Estuarine Sediment Communities,” Applied and Environmental Microbiology, Vol. 71, No. 4, 2005, pp. 2036-2045. http://dx.doi.org/10.1128/AEM.71.4.2036-2045.2005
[18]	S. Dhanasekaran, T. M. Doherty and J. Kenneth, “Comparison of Different Standards for Real-Time PCR-Based Absolute Quantification,” Journal of Immunological Methods, Vol. 354, No. 1-2, 2010, pp. 34-39.
[19]	J. A. Whelan, N. B. Russell and M. A. Whelan, “A Method for the Absolute Quantification of cDNA Using Real-Time PCR,” Journal of Immunological Methods, Vol. 278, No. 1-2, 2003, pp. 261-269. http://dx.doi.org/10.1016/S0022-1759(03)00223-0
[20]	B. McKew, A. J. Dumbrell, S. D. Daud, L. Hepburn, E. Thorpe, L. Morgensen and C. Whitby, “Characterization of Geographically Distinct Bacterial Communities Associated with the Coral Mucus from Acropora spp. and Porites spp,” Applied and Environmental Microbiology, Vol. 78, No. 15, 2012, pp. 5229-5237. http://dx.doi.org/10.1128/AEM.07764-11
[21]	N. Rajendran, O. Matsuda, Y. Urushigawa and U. Simidu, “Characterization of Microbial Community Structure in the Surface Sediment of Osaka Bay, Japan, by Phospholipid Fatty Acid Analysis,” Applied and Environmental Microbiology, Vol. 60, No. 1, 1994, pp. 248-257.
[22]	T. Stoeck, I. Kroncke, C. A. Duineveld and Palojarvi, “Phospholipid Fatty Acid Profiles at Depositional and Non-Depositional Sites in the North Sea,” Marine Ecology Progress Series, Vol. 241, 2002, pp. 57-70. http://dx.doi.org/10.3354/meps241057
[23]	D. L. Balkwill, F. Leach, J. T. Wilson, J. F. Mcnabb and D. C. White, “Equivalence of Microbial Biomass Measures Based on Membrane Lipid and Cell Wall Components, Adenosine Triphosphate and Direct Counts in Subsurface Aquifer Sediments,” Microbial Ecology, Vol. 16, No. 1, 1988, pp. 73-83. http://dx.doi.org/10.1007/BF02097406
[24]	J. Guezennec and A. Fiala-Medioni, “Bacterial Abundance and Diversity in the Barbadose Trench Determined by Phospholipid Analysis,” FEMS Microbiology Ecology, Vol. 19, No. 2, 1996, pp. 83-93. http://dx.doi.org/10.1111/j.1574-6941.1996.tb00201.x
[25]	S. D’Hondt and S. Rutherford, “Metabolic Activity of Subsurface Life in Deep Sea Sediments,” Science, Vol. 295, No. 5562, 2002, pp. 2067-2070. http://dx.doi.org/10.1126/science.1064878
[26]	D. M. Alongi, “Vertical Profiles of Bacterial Abundance, Productivity and Growth Rates in Coastal Sediments of the Central Great Barrier Reef Lagoon,” Marine Biology, Vol. 112, No. 4, 1992, pp. 657-663. http://dx.doi.org/10.1007/BF00346184
[27]	G. M. Luna, E. Manini and R. Danovaro, “Large Fraction of Dead and Inactive Bacteria in Coastal Marine Sediments: Comparison of Protocols for Determination and Ecological Significance,” Applied and Environmental Microbiology, Vol. 68, No. 7, 2002, pp. 3509-3513. http://dx.doi.org/10.1128/AEM.68.7.3509-3513.2002
[28]	F. Inagaki, M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, K. H. Nealson and K. Horikoshi, “Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk,” Applied and Environmental Microbiology, Vol. 69, No. 12, 2003, pp. 7224-7235. http://dx.doi.org/10.1128/AEM.69.12.7224-7235.2003
[29]	S. R. Prabagaran, R. Manorama, D. Delille and S. Shivaji, “Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in Seawater Collected off Ushuaia, Argentina, Sub-Antarctica,” FEMS Microbiology Ecology, Vol. 59, No. 2, 2007, pp. 342-355. http://dx.doi.org/10.1111/j.1574-6941.2006.00213.x
[30]	J. Heider, A. M. Spormann, H. R. Beller and F. Widdel, “Anaerobic Bacterial Metabolism of Hydrocarbons,” FEMS Microbiology Reviews, Vol. 22, No. 5, 1999, pp. 459-473. http://dx.doi.org/10.1111/j.1574-6976.1998.tb00381.x
[31]	M. Boll, G. Fuchs and J. Heider, “Anaerobic Oxidation of Aromatic Compounds and Hydrocarbons,” Current Opinion in Biotechnology, Vol. 6, No. 5, 2002, pp. 604-611.
[32]	S. Sehnell and B. Sehink, “Anaerobic Aniline Degradation via Reductive Deamination of 4-Aminobenzoyl-CoA in Desulfobacterium anilini,” Archives of Microbiology, Vol. 155, No. 2, 1991, pp. 183-190.
[33]	J. D. Coates, J. Woodward, J. Allen, P. Philip and D. R. Lovley, “Anaerobic Degradation of Polycyclic Aromatic Hydrocarbons and Alkanes in Petroleum-Contaminated Marine Harbour Sediments,” Applied and Environmental Microbiology, Vol. 63, No. 9, 1997, p. 3589.