title: 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.
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 C(5) and C(16) 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.
authors.affiliation: Helmholtz Zentrum München--Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Department of Terrestrial Ecogenetics, Institute of Soil Ecology, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany. perezdemora@gmail.com
authors.forename: Alfredo
authors.initials: A
authors.lastname: Pérez-de-Mora
authors.forename: Marion
authors.initials: M
authors.lastname: Engel
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
mesh_terms: D000473:Alkanes / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics*; D001673:Biodegradation, Environmental; D018533:Biomass; D016000:Cluster Analysis; D042926:Cytochrome P-450 CYP4A / Q000235:genetics / Q000378:metabolism; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D005798:Genes, Bacterial; D005838:Genotype; D005858:Germany; D006838:Hydrocarbons / Q000378:metabolism; D008670:Metals / Q000378:metabolism; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D012987:Soil / Q000032:analysis; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*; D014197:Trees / Q000382:microbiology
chemical_list: D000473:Alkanes; D004269:DNA, Bacterial; D006838:Hydrocarbons; D008670:Metals; D012987:Soil; D012989:Soil Pollutants; D042926:Cytochrome P-450 CYP4A