MaCuMBA Conference June 27-30, 2016 Berlin, Germany
From simple to complex degradation of hydrocarbons. A concept of metagenome succession in oil-amended microcosms Session 2: Novel (meta)genomic approaches in marine microbiology
Deni Ribicic1, Odd Gunnar Brakstad2, Roman Netzer2, Terry C.Hazen3, Finn Drabløs1 Norwegian University of Science and Technology, Department of Cancer Research and Molecular Medicine, Trondheim, Norway1, SINTEF Materials and Chemistry, Department of Environmental Technology, Trondheim, Norway2, University of Tennessee Knoxville, Department of Civil and Environmental Engineering Knoxville, USA3
[email protected]
Berlin, Germany
June 28-30, 2016
Introduction •
Natural or anthropogenic introduction of HCs to marine environments
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Different types of oil spills, Exxon Valdez (surface), DWH (sub-surface)..
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Diversity of processes shaping weathering of spilled oil
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Biodegradation – a process facilitated by microorganisms
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«Molecular machinery» employed by microorganisms
Surface release
Sub-surface release
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Berlin, Germany
June 28-30, 2016
Introduction PETROLEUM
Aliphatics •
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Aromatics
Alkanes (paraffins)
Branched alkanes (isoprenoids)
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Monocyclic aromatics
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Polycyclic aromatics
Cycloalkanes (naphtenes)
linear alkanes > branched alkanes > small aromatics > cyclic alkanes > HMW aromatics (Das & Chandran, 2011)
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Berlin, Germany
June 28-30, 2016
Introduction Plethora of HC-transforming genes and enzymes can be found in oil-contaminated environment
Aliphatics
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Aromatics
C1-C4- variety of soluble and particulate methane monooxygenases
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C5-C16- heme-containing cytochrome P450 CYP153 and non-heme di-iron alkane hydroxylases
Different types of monooxygenases and dioxygenases Naming- compound accordignaly , eg. Xylene-XMO, Naphtalene-NDO, BiphenylBPDO, Benzoate- BDO, etc.. (Peng et al., 2008)
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> C17- uknown enzyme systems (Beilen & Funhoff, 2007)
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Berlin, Germany
June 28-30, 2016
Concept of metagenome successions • Relies on general principle of ecological succession
• Analogous to the microbial community succession
Simple
Complex
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Berlin, Germany
Concept of metagenome successions
• Oil biodegradation experiments or real oil spill situations • Microbial community shifts • Microbes associated with degradation of different oil compounds
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June 28-30, 2016
Berlin, Germany
June 28-30, 2016
Concept of metagenome successions
Simple
Complex
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Berlin, Germany
Metagenome dynamics during oil biodegradation • Five samples for metagenome sequencing- NS (controls) and NSOD (oil incubations) • Venn diagram reveals unique and shared functions • Significantly higher abundance of gene fragments putatively encoding for motility and chemotaxis, nitrogen and iron metabolism 8
June 28-30, 2016
Berlin, Germany
Metagenome dynamics during oil biodegradation
• Gene products involved in degradation of short- and long- chain alkanes succeeded by genes involved in transformation of BTEX and PAHs
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Correlation between HC genes and pattern of HC that are likely to be degraded by respective genes
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June 28-30, 2016
Berlin, Germany
June 28-30, 2016
Summary
Abundance
• Similar to the microbial community shift, a shift of hydrocarbon degrading genes occurs throughout the oil incubation experiment • The metagenome shift resembles the general principle of succession where there is a development from a simple to the complex structure. • Sequences (putatively) encoding gene products responsible for degradation of alkanes are substituted by sequences encoding genes products responsible for degradation of aromatics and PAHs
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Thank you!
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Berlin, Germany
June 28-30, 2016
References Beilen, J. B., & Funhoff, E. G. (2007). Alkane hydroxylases involved in microbial alkane degradation. Applied Microbiology and Biotechnology, 74(1), 13-21. doi: 10.1007/s00253-006-0748-0 Peng, R.-H., Xiong, A.-S., Xue, Y., Fu, X.-Y., Gao, F., Zhao, W., . . . Yao, Q.-H. (2008). Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiology Reviews, 32(6), 927-955. doi: 10.1111/j.15746976.2008.00127.x Das, N., & Chandran, P. (2011). Microbial Degradation of Petroleum Hydrocarbon Contaminants: An Overview. Biotechnology Research International, 2011. doi: 10.4061/2011/941810
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Experimental setup
Oil biodegradation in microcosms under cold water temperature (5 ˚C) and smal oil droplet size (10-20 µm) dispersed with chemical dispersant
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June 28-30, 2016
Berlin, Germany
How can we make this data useful?
June 28-30, 2016
Berlin, Germany
How can we make this data useful?
June 28-30, 2016
Berlin, Germany
How can we make this data useful? •
Modelling
June 28-30, 2016
Berlin, Germany
June 28-30, 2016
How can we make this data useful?
Microbial community composition
Incubation day
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Chemical composition
