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Abundance and Diversity of n-Alkane-Degrading Bacteria in a Forest Soil Co-Contaminated with Hydrocarbons and Metals: A Molecular Study on alkB Homologous Genes

  • Soil Microbiology
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Abstract

Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C5 and C16 at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.

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Acknowledgments

Dr. Pérez-de-Mora thanks the Spanish Ministry of Education and Science (MEC) for the fellowship.

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Authors and Affiliations

  1. Helmholtz Zentrum München—Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Department of Terrestrial Ecogenetics, Institute of Soil Ecology, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany

    Alfredo Pérez-de-Mora, Marion Engel & Michael Schloter

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  1. Alfredo Pérez-de-Mora
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  2. Marion Engel
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  3. Michael Schloter
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Correspondence to Alfredo Pérez-de-Mora.

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Figure S1

Relative T-RF patterns of the alkB gene in soil samples from the different zones of contamination (small letters a–e indicate field replicates from the corresponding sites). C B control zone, X B1 highly contaminated zone, X B2 and X B3 intermediately contaminated zones (RTF 372 kb)

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Pérez-de-Mora, A., Engel, M. & Schloter, M. Abundance and Diversity of n-Alkane-Degrading Bacteria in a Forest Soil Co-Contaminated with Hydrocarbons and Metals: A Molecular Study on alkB Homologous Genes. Microb Ecol 62, 959–972 (2011). https://doi.org/10.1007/s00248-011-9858-z

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